Yamanote line, 1am-5am
'Inner circle' (counter-clockwise, from Shinjuku toward Shinagawa, from Tokyo toward Ueno): departures every 15 minutes
'Outer circle' (clockwise, from Shinjuku toward Ikebukuro, from Tokyo toward Shinagawa): departures every 15 minutes
Keihin-Tohoku, Negishi lines, 1am-4am
Omiya-Sakuragicho: departures every 20-50 minutes
Chuo line (rapid), 12am-4am
Mitaka-Takao: departures every 30-60 minutes
Chuo-Sobu line, 12.30am-5am
Mitaka-Chiba: departures every 10-80 minutes
Ome line
Departing Tachikawa: 2am, 3.20am
Departing Mitake: 3am, 4.38am
Note that trains don't stop at Miyanohira, Hinatawada, Ishigamimae, Futamatao, Ikusabata and Sawai stations.
Sobu Main line, Narita line
Departing Chiba: 1.20am, 3.15am
Departing Narita: 2.10am, 3.55am
Note that trains don't stop at Higashi-Chiba Station.
Yokosuka line, 1am-5am
Yokohama-Zushi: departures every 80 minutes
Note: there are no late-night services for Saikyo, Takasaki, Utsunomiya, Shonan-Shinjuku, Keiyo, Joban and Narita lines.