TY Harbour brewpub, 2-1-3 Higashi-Shinagawa.  Open 11:30-14:00 and 17:00 onwards

Fairly easy to find once you're in the right area, if that makes sense!  Take the Monorail to Tennozu Isle station, exit into the elevated walkways, and you'll see a whole load of signs dotted around the place plus some maps, amongst which are directions to the brewpub.  Basically, get down to street level, find the waterfront, then head away from the monorail to the bridge and you'll see it.

In an area of office towers, this place makes it's money from workers in the afternoon when the bar area is closed and you need to wait for a table in order to scoop!  It's expensive but worth a visit as Tokyo has so few brewpubs, although the beers (one on cask) aren't great.
 

Sumidagawa Brewery Pub, Azumabashi 1-23-36, 3F. Open 11:30am-2, 5-9pm daily. 

Situated across the Sumida river from Asakusa metro (Asakusa or Ginza line).  Once at the waterfront cross the river heading for the "giant golden sperm"... you'll know when you see it!  The brewpub is in the building although it's not obvious at all and whether they brew or not is another matter, although we did see their dark beer on tap in Popeye!

There's a three-beer sampler for Y980 so don't believe them when they say it's big glasses or nothing! And you won't want more than the little samplers, believe me, as this place is owned by Asahi with all the negative implications you could imagine! There's a French restaurant on 4FL, a beer hall on 2FL, and a bar on 1FL.).   We went to the standing bar on the 1st floor, the kit is visible through windows although I'm not totally convinced they actually brew there.

 

Bakusyu Club Popeye, 2-18-7 Ryogoku. Open 17:00-01:00 (Sat. to 2am). Closed Sundays.

Exit Ryogoku station and head away from the Sumo stadium.  Basically, the bar is one block south of the station on a side-road up a set of steps and, once you've been once, very easy to find.  Put it this way; compared to some other Tokyo bars I could have found it blindfold...

Quite simply, one of the world's best beer bars!!!   The only real "scooper's" pub in Tokyo and almost certainly the best bar between One Pint Pub in Helsinki all the way across frozen Siberia to the west coast of America... the best bar for more than 6000 miles is an enviable position to be in!  Aoki-san runs a great bar which has 70 beers on tap including 3 cask ales and you can even order a 10-glass sampler from the menu (also in English).  It's not cheap but, for the experience of being in the best scooper's pub for thousands of miles and the excellent range of Japanese craft beer on sale, Popeye's is a must-visit. Make sure if you're going to re-visit you get a "member's card"!   I'll say it again - Popeyes is one of the world's best beer bars.

 

Baird's Nakameguro taproom, Nakameguro GT Plaza, C-Block, 2nd Floor, 2-1-3 Kamimeguro, Meguro-ku

To find it, leave Naka-Meguro station (W end of Hibiya subway line, station H01) then walk under the modern building and you'll see the taproom up on the balcony of the building ahead. To reach it, go to the left-hand side of this building, go up the stairs, and you'll come to the balcony with the bar at the far end.   Well worth a trip out here for some excellent beers.

Bairds' flagship bar in Tokyo with around 20 Bairds beers on sale including some on cask; a wide range of quality brews with some stunners in the line-up.

 

Thrash Zone, Tsuruyacho 2-19-8, Paseri Bldg 2F, Yokohama. Open 6pm-2am, closed Sundays.

Difficult to find bar on the 2nd floor of a nondescript building!  Head North from the station (past the Excel hotel) over a river with the expressway overhead, then it's the third turn on your left, up a tiny lane, and up some stairs on your right.  I didn't navigate to this one so good luck - but make sure you get there, it's simply stunning!

Oh yes, oh yes, oh yes... This is what I went to Japan for, a minuscule bar up a dingy stairwell with no signs (well, there may have been in Japanese...) with barely enough space for 20 people yet, somehow, the master keeps 12 beers on tap!!!   American classics (Green Flash are regular) along with Japanese micros and even a house beer, the mega-hoppy "Crossover" brewed for them at Yokohama brewpub.   No food apart from pickled stuff (!) but it's the beer you're here for and there aren't many better beer bars than this one. An absolute stunner, especially if you like hops!

Gambrinus, 6th floor, 3-16-5, 46-Tokyo-bldg, Kokubunji-shi

A fair way out of the centre (21km), but worth it.  Take the Chuo line from Tokyo or Shinjuku to Kokubunji (7 stops west of Ogikubo mentro on the Marunouchi line) which runs every 6 mins or so, takes around 25 mins, and costs ¥380.

13 Japanese craft beers on tap at this friendly and relaxed bar up in the sky.  Some great Japanese beers on tap, well worth the trip out here on the Chuo line to Kokubunji station, and the landlord is extremely sociable and speaks some English too.  A highly recommended trip out of the centre for a good range of beer.

 

Ushi-Tora, Sankyu Building 2F Kitazawa 2-9-3.  Closed 1st and 4th Tuesdays. Open Wed-Mon 17:00-01:00 Tues closed.

Take the Keio Inokashira Line from Shibuya to Shimokitazawa (4th stop, very frequent), or you can take the Chiyoda metro to the westernmost terminus of Yoyogi-uehara and take the Odayuku line one stop further out; it's annoyingly close to the metro system but not quite within reach!

Twenty beers on tap, most of them local microbrews, with some on cask too.  On a balcony and accessed by stairs, this is a superb bar with an excellent beer list although it's very expensive even for Japan!  Worth going for the range of beer which includes some real rarities you won't see anywhere else, even in Popeye.

 

Craft Beer Bar, Yokohama-shi, Naka-ku, Aioi-cho 2-31-3. Open 4-11:30pm (noon-10pm weekends). Closed Mondays.

From the front exit of Kannai JR station (when heading out of Yokohama) head into the centre, cross the main road, and keep going.  When you pass the Lawson shop it's the 4th on your left with the bar 50 metres on your right.  Hard to find.

Great little bar with barely room for 20 people, is a must-visit when in Yokohama and has some excellent microbrews on tap and handpump.  Close to Yokohama brewery tap so well worth a look, although it's not that easy to find!  The beer board is in Japanese but someone should be able to decipher them for you...

 

Towers standing bar, Yaesu 2-8-10.  Open 5:30-11pm, closed weekends.

From Kyobashi station on the Ginza metro line surface onto Chuo-Dori, the main road and head south towards the overbridge.  At the big crossroads head right down the road flanked by thin trees until you see a road on your left with a "Fed-Ex Kinkos" office next to it.  Head down here and the bar is almost immediately on your right.

Eight or so excellent draught Japanese beers are available in this tiny place (it really is small, even for Japan, and can probably accomodate 10 thin people!) which often has some US beers too. An amazing beer range for such a small bar, plus the owner speaks some English and is very sociable!   A must-visit, but note it's closed weekends.

 

Aldgate, Shin-iwasaki building 3rd floor, 30-4 Udagawa-cho Shibuya-ku.  Open 18:00 onwards.

This one is best done at night just to get the full-on Shibuya experience of a million blazing neon lights and melee of people!  Exit Shibuya JR station and head for the famous square with the old subway coach and little dog statue.  From here, cross the famous ever-busy crossing straight across from the station down the small alley with a big HMV building at the end.  Carry on along the lane, past McScum with it's huge "bag of fries" sign, and opposite a red-striped building you'll see a Union Jack flying on your right.  Go up 2 flights of stairs and you're there... but do it in darkness!

Around 16 beers on tap including some Japanese micros amongst some piss-poor UK beers such as Greede Kerching and Fullers.  You should find scoops here, plus the current house beer is from Swan Lake and very nice indeed.   Look for the Union Jack fluttering above some stairs on a very crowded, neon-lit and busy street, go up two flights and you'll find the pub.

Bacchus, Yaesu 1-7-7, Dai-ni Yamamoto Bldg B1F. Open 5pm-midnight (-3am Fridays). Closed Sundays.

Leave Tokyo station.  Opposite the huge white tower is a lane with a red & green signed building alongside it; go along here almost to the next junction and the cellar bar is on your right and not that obvious!  Alternately, from Nihombashi metro (Ginza line is closest, Tozai and Asakusa lines also stop here) head south along the main road until you reach a building with huge columns on your right.  Turn right down the lane and the bar is immediately on your left.

Nice little cellar bar (look for the stout sign on the wall outside and blue lights) which has some cask ales plus guest Japanese beers on tap and some more bottles in the fridge; well worth a look.

 

Bicke, Kichijoji Honcho 2-13-7, Grandale Bldg 3F.  Open 17:00-midnight (from 13:00 weekends), closed Wednesdays.

Leave Kichijoji station and walk left along the road until you reach a main junction, where you turn right.  Go along here to the second lane on your left, walk along there for 100 metres or so looking for the sign outside a tall building.  Take the lift to the 3rd floor, turn left, and you're there. 

Relaxed bar (this one on the 3rd floor) with a good Japanese tap range plus some others in bottle; a good speciality beer bar which features craft beers from around the world along with a rotating selection of Japanese microbrews.  Only five minutes from Holic.  Kichijoji is on the JR Chuo line, sociably on the way to Kokubunji and the superb Gambrinus, making a train crawl possible!  It's only 18 mins from Shinjuku, 210¥.

 

Shinshu Osake Mura (Nagano Sake Village), Shimabashi Eki-mae Ichigokan 1F, Shimbashi 2-20-15.  11am - 9:30pm, closed Sun, 2,3rd Sat and Holidays.

Not easy to find, but find it!!  It's in the Shimbashi Eki Mae building, across the street from the Shiodome entrance to Shimbashi station, on the 1st floor "Not far from the entrance with the racoon with the huge testicles; you'll know it when you see it" says Chuwy from Tokyo!

This is a bar run by the prefecture (basically a county) of Nagano and it sells micro-brewed beer and sake from that county. There are around 15 beers (which vary) and 40-50 sakes which are available by the tasting glass making this a proper "sake scooping bar!".  The beers can be rare, with some not seen elsewhere in Tokyo. The food is cheap, too, and traditional including horse, wasabi greens and pickled stuff. Above all it's cheap, being a standing bar, and drinking in is the same price as take-away making it an absolute bargain.   They also have Ume, a liquor made with the ume plum, which is gorgeous and maybe also unfiltered sake - very rare.   Overall, a superb and very different place and well worth finding.

 

Bulldog Beer Bar, Ginza 3-1, Ginza INZ #1, 1F. Open 11:30am-2, 5-11:15pm daily.

Just outside Yurakucho JR (and Yurakucho metro line) station.  Head towards the elevated motorway from the station and you can't miss it, if you do there's an entrance under the bridge itself!  The bar is on the 1st floor of the INZ shopping centre.

Bulldog has around ten beers on tap including American micros and local stuff, as well as some good bottles.

 

Griffon, 2-22-6 Shibuya, Shibuya-ku.  Open from 17:00 daily.

Shibuya station is fucking huge so expect to get lost and/or confused!  Exit to the main square full of buses and head left towards the elevated motorway.  At the big junction turn left and follow the path under the railway then across the shambolic main road covered in concrete flyovers and suchlike, carry on for 100 metres and you'll see a big red sign with "ECC" on it on your left.  There should be some steps down into the bar here!

Yet another cellar bar, look for the signs just inside the building. A new bar with around a dozen Japanese micros on tap at high prices but there are some decent beers in there so it's worth a stop.  

 

BarBAR, Marunouchi 1-9-1, Kurobei Yokocho (B1F). Open 11am-11pm daily.

In the depths of Tokyo station and hard to find!  Basically, find the Shochu shop in the food area then go down the stairs and you'll find the bar in the opposite direction to Shochu. There are maps which will guide you, but it still took us a good 10 minutes to find!!

A decent selection of Japanese microbrews by the bottle (Y100) and a few microbrews on tap make this hard-to-find bar a worthy stop and you'll be passing through Tokyo station at some point so you may as well!

 

Maltan, Uchi-Kanda 3-13-10, Green Bldg B1F. 18:00 onwards

Exit the JR station into the melting pot of Kanda's pachinko parlours.  Turn left and follow this fascinating lane south until you reach "Pachinko club Hikari" on your left whereupon look for the sign in the street and picture of a whisky glass on your right by a green building.  It's another of those basement bars with a lot of character and I liked it a lot.

Right in the middle of Kanda, a fascinating, vibrant place with probably my favourite street in the whole city running along the west side of the railway - a total culture shock yet endlessly fascinating.  As for the bar, well it has a good Japanese beer range including a house stout from Minoh which is excellent.  There are cask ales too plus a wide range of whisky, hence the name, and it's yet another cosy cellar bar.

 

Holic, Kichijoji Minamicho 1-1-8, Keyaki Bldg B1F. Open 7pm-5am; Sat/Sun 6pm-5am daily.

Take the southern exit from Kichijoji station and turn right.  Walk along the narrow lane until you come to the point where it reaches a main road and the cellar bar is on your right just before the junction.  Alternately, from Bicke walk back towards the station but, rather than turn left to reach it, continue under the railway and then turn immediate left.  50 metres along here is the junction described above.

Basement bar (yes, another one!) with a few Japanese beers on tap/bottle but it really focusses on foreign brews in bottle. Worth a stop if you're here for Bicke.

 

Konne, Yoyogi 2-2-1, Southern Terrace, Shinjuku.  Open 11am-9pm daily.

Once at Shinjuku station follow signs for the Southern Terrace exit and, if you're good with geography and with a bit of luck, you'll find it.  Look for the big "My Lords" sign and you're not far off and if you can see the tall pointy building you're doing well too.

This is really a shop selling souvenirs from Miyazaki Prefecture in Kyushu although there's also a small bar area where you can drink Miyazaki microbrew beers along with very tasty charcoal-grilled free-range Kyushu chicken (Y1150 for beer and yakitori).  Note that you need to put money in the vending machine, press the appropriate button then take the ticket to the bar to order stuff.   Unusual, but well worth a visit for the delicious chicken and beers you won't see anywhere else in town.

 

Tanakaya beer shop, Mejiro 3-4-14.  Open 11am-8pm. Closed Sundays.

On Mejiro-dori just a few seconds west of Mejiro station.

Beer shop with loads of USA and some Japanese micro beers.   We didn't visit but were told it's pretty good.

 

Tokyu department store, Shinjuku station.

Head for the underground shopping areas and you'll find the Tokyu store, the drinks section is surprisingly small and difficult to find but worth the effort.

Hidden in the labrynthian depths of this huge and confusing station (one of the busiest in the world) is this huge department store with a mammoth drinks section. You'll find a small range of craft beer in the fridges, mainly in cans, so it's not worth a special trip although if you're there...

 

Hotel recommendations

One thing to remember is that, when entering almost any hotel apart from westernised ones (the Oak counts in this category) you'll see a small step inside the door.  Remove your shoes before you climb this and select a pair of slippers from the lockers or rack there; these are to be worn when about the hotel and outside shoes must only be put on when you're leaving in the place you took them off - to keep them on is very bad manners and will get a ranting!

 

Oak Hotel, 6-1-2, Higashi-Ueno.

Small backpacker-style hotel with small rooms complete with tiny plastic ensuite facilities.  Close to Inaricho (Ginza line) metro station, exit the platforms and walk along the main road under the pedestrial bridge.  Shortly after this you'll see a gap in the buildings on your left (by a writing paper shop) and the hotel is the redbrick building along the path.

It's clean, close to Ueno or Inaricho metro stations, plus only two stops from Popeyes too! Very much a foreigner-oriented place but I'd stay there again; ¥8,500 ensuite twin if you book online via the site.

 

Capsule hotel Asakusa Riverside, 2-20-4, Kaminarimon

Easy to find, only 2 minutes walk from exit 4 of the Ginza line station. Come out of exit, turn right along the small lane, and it's the first tall building on your right. Go up 2 flights of steps to find reception where you'll need to pay via a vending machine (the button marked "sleep", I think it was the only one in English!

There's a communal bath on the 9th floor with great views over the Sumida river and the passers by on the bridge get to see you undress via the windows too!  A great way to experience a capsule, as you should - it's much better than you'd imagine and very cheap!  Foreigners (Gaijin) generally get put on floor 5 and ladies have their own floor.  A bargain ¥3000 per night for a capsule and all the accompaniments such as towels and gown, just do it! 

 

Hotel New Azuma, 2-38-3,Kiyokawa,Taitoku.

From Metro station Minami-Senju (Hibiya line) walk down the station steps then back up onto the bridge ahead. Take the first steps down on your left (facing the freight yard) then turn right at the bottom.  Head along this street to the big crossroads, cross over, then take the first narrow road on the left and the hotel is about 100m along on your left. 

A small backpacker's hotel and/or businessman place with small traditional rooms (3 tatami mats in size, which is about 2 metres by 3) complete with aircon, TV and futon.  It has cooking and washing facilities, free green tea plus a superb hot and very powerful shower (as well as a proper Sento bath) so, for the price, it's hard to beat.  If you want slightly more luxury the Maruchu you'll pass on the way seems more upmarket.   The only issue is that you're well north of the centre, but the Hibiya metro line station is only 5 minutes away giving access to all the city so it's your choice!  Only ¥3000 single for a traditional 3-tatami mat room with a rice husk pillow and bathrooms along the hall.  More a backpacker's hotel than a traditional Japanese one although it does retain some aspects such as having to wear slippers when coming in. 

 

Maruchu, 3-2-2 Minamisenjyu

You'll pass this hotel on your way from Minami-Senju station to the New Azuma as described above.

This was full when we tried to stay, but it looks like a decent enough business hotel.  ¥3500 / night (¥3300 3 nights), twins ¥5000 / night.  Curfew 01:00