A work in progress, to be sure, but you are sure to find a decent beer pub, bottle shop...as well as British, Irish, Belgian, German etc. pubs, and beer gardens on this page.
I'm afraid my website doesn't have a search function, so I've listed places by city or city ward. Just scroll until you find your area. Most venues have links to their website, Instagram, Facebook page, etc. Just in case, here's a link to Google Maps!
Venue Key, according to city or city ward: e.g. 荒川 Arakawa The nearest train station follows, in [brackets]: e.g. [Nippori]
Venues with asterisks: (*) have SOMEthing on tap -- maybe three, maybe two, maybe only one! This place may serve cans/bottle selections, but do have a limited selection from a keg. (**) have Nothing on tap. This may include bottle shops, beer stores, and other places that sell craft beer in bottles & cans, but don't expect anything poured from a keg.
AWAYA**
[Kita-senju]
Beer-ma Kita Senju
[Kita-senju]
BURGHACK**
[Ayase]
Craft Beer "abbina"
[Keisei Tateishi]
Sakazuki Brewing
[Kita-Senju]
Puedobar**
[Kita-Senju]
UNDERGROUND CRAFT BEER AKABANE
[Akabane]
Z BURGER & CBT EQUiA**
[Kita-Senju]
Akatsuki Taps Ginza
[Ginza]
Antenna America Tokyo
[Tokyo]
Craft Beer Bar IBrew Ginza
[Ginza-itchome / Kyobashi]
Craft Beer Market Mitsukoshi-mae
[Mitsukoshi-mae]
Craft Beer & Whisky Bar Hatchobori Garden
[Hatchobori]
bar HERME
[Nishi-Kasai]
Beer Bar GARAGE
[Ichinoe]
cerdo
[Kasai]
Donguri**
[Kasai]
Huckle Berry
[Mizue]
Keisei Koiwa Craft Liquor Store*
[Keisei Koiwa]
KOIWA BUSH BASH**
[Koiwa]
Cranc Brewing
[Itabashi-Kuyakushomae]
GuuNeeds**
[Motohasunuma]
Tokyo Aleworks Taproom Itabashi
[Shimo-Itabashi]
abbina
[Keisei Tateishi]
Beer Bar CROWD
[Shin-Koiwa]
Bistro Hahifuya*
[Keisei Tateishi]
Keisei Koiwa Craft Liquor Store**
[Keisei Koiwa]
Kichi Brewing
[Horikirishobuen]
Abbot's Choice Machida
[Machida]
Beer Bulk J
[Seiseki-Sakuragaoka]
Beer House Ken*
[Fuchu]
Beer Pub 25
[Mitaka]
Cafe & Craft Beer Adaya
[Fuchu]
Craft Beer & Wine & Chicago Pizza U-!
[Tachikawa]
Craft Beer Cafe Prost
[Hachioji]
Craft Beer Market Kichijoji
[Kichijoji]
Oga Brewing
[Mitaka]
Sakamichi Brewing
[Tachikawa]
Tachihi Brewery
[Tachihi / Takamatsu]
Wine & Craft Beer Halbar
[Tachikawa]
American Pizza & Craft Beer TRUNK
[Chibachuo]
Astore Wine & Craft Beer
[Nagareyama-otakanomori]
Bar HOP
[Keisei Funabashi]
Beer and Ale Latta
[Nishi-Chiba]
Beer Brain Brewery Taproom
[Kashiwanoha-Campus]
Beer O'clock
[Chibachuo / Keisei Chiba]
Bistro Recolte
[Chiba / Chibachuo]
Cafe & Bar Cluster
[Kashiwa]
Choshi Cheers
[Inubo]
Funabashi Beer
[Kaijin / Keisei-Nishifuna]
Gastro-Pub, The OFFice Hours
[Chibachuo]
GLOBAR
[Kashiwa]
Kashiwa Ale*
[Minami-Kashiwa]
Kashiwa Beer (Komainu Brewery Taproom
[Kashiwa]
Kyonan Beer**
[Hota +500m]
THE LIFE
[Kashiwa]
Loco Beer
[Chiku Center / Yukarigaoka]
82 Ale House
[various]
Affenbar PUB
[Toranomon Hills / Uchisaiwaicho]
The Aldgate British Pub
[Shibuya]
Beerpub Nonsuch
[Ikebukuro]
British Pub&Bar The Cluriaune
[Nishi-Shinjuku / Seibu Shinjuku]
THE FooTNiK
[Ebisu]
Full Monty British Pub & Cider House
[YOKOHAMA - Hinodecho stn]
Good Heavens!
[Shimo-Kitazawa]
HIGHBURY
[Shinjuku-gyoemmae]
Hobgoblin British Pub - Roppongi
[Roppongi]
Hobgoblin British Pub - Shibuya
[Shibuya]
The Hole in the Wall
[Nishi-Ogikubo]
Hub British Pub (multiple locations)
[Plz check Google maps!]
The Mermaid
[Akasaka-Mitsuke]
British Pub Publion
[Shimokitazawa]
The Rising Sun
[Yotsuya]
The Royal Scotsman
[Iidabashi / Ushigome-kagurazaka]
British Pub 2nd Half
[Takadanobaba]
The Tavern
[YOKOHAMA]
The Tipplers Arms
[Azabu-Juban]
The Warrior Celt
[Keisei Ueno / Okachimachi]
What the Dickens!
[Ebisu]
Aceboon Public House
[Higashi-Kitazawa / Sasazuka]
An SOLAS
[Yoyogi]
Celts
-Shinbashi Hibiyaguchi [Shinbashi]
-Shinbashi Karasumoriguchi [Shinbashi]
-Yaesu [Tokyo]
-Yokohama Kannai [Kannai]
Clann
[Jiyugaoka]
The Cluracan
[Koenji]
County Clare
[Tachikawa]
Craic Akasaka
[Akasaka / Tameike-Sanno]
The Dubliners
[Ikebukuro]
Failte
[Shibuya]
The Harp
[Nakano]
Irish Pub Peter Cole - Nishi-Shinjuku
???
Irish Pub Peter Cole - Kanda
???
KENNY'S
[Chofu]
Kildare
[Machida]
Laser Rush
[Motomachi-Chugakai]
MAN IN THE MOON
[Shimbashi]
Mulligans
[Kamiyacho]
Sceal eile
[Ryogoku]
ROGUE
[Kichijoji]
Seamus O'Hara
[Musashi-Koyama]
Shamrock
[Roppongi]
The Shannon's
[Osaki]
TULLAMORE
[Yoyogi-Hachiman]
The Warrior Celt
[Okachimachi]
The World End Irish Pub
[Keisei Ueno / Ueno]
Ye Malthouse
[Naka-Meguro]
The Yoke
[Mizonokuchi]
82 Ale House
Forest Beer Garden Apr.??-Sep.??
[Harajuku]
Ginza Lion
Hub British Pub
Kirin City
The Rose & Crown
[Takeshiba]
SCHMATZ
Spring Valley Brewery
World beer museum
[Oshiage / Tokyo Skytree stations]