On special occasions, typically around holidays, the Tokyo Metro Hibiya Line and Namboku Line operate special , formerly known as , direct through services to the Minatomirai Line. From 2012, the Tokyo Metro Fukutoshin Line will also inter-run to/from the Minatomirai Line.
Although the Minatomirai Line runs entirely underground, it is separate from the Yokohama Municipal Subway, which is operated by the Yokohama City Transportation Bureau.
| Station Name | Local 各停 | Express 急行 | Commuter Express 通勤特急 | Limited Express 特急 | Transfers |
|---|---|---|---|---|---|
| Continues to/from Tōkyū Tōyoko Line, through service to Shibuya Station | |||||
| Yokohama Station | Tōkyū Tōyoko Line (through service to Shibuya Station) Tōkaidō Main Line, Yokosuka Line, Keihin-Tōhoku Line, Negishi Line, Keikyū Main Line, Sagami Railway Main Line, Yokohama City Subway Line 3 | ||||
| Shin-Takashima Station | |||||
| Minato Mirai Station | |||||
| Bashamichi Station | |||||
| Nihon-ōdōri Station (Kenchō-Ōsanbashi) | |||||
| Motomachi-Chūkagai Station (Yamashita-kōen) | |||||