Minatomirai Line

Operations are managed by Tokyu Railways, with no changing of staff at Yokohama Station; Tokyu staff (train drivers and conductors) continue to support the train over the Minatomirai portion of the line as well. Station-side staffing is provided by Minatomirai employees with the exception of Yokohama Station, which is managed by Tokyu Railways. Many Minatomirai employees are former employees of Tokyu Railways. Train management is controlled by Yokohama Minatomirai Railway Company at an operational command center. Railway facilities are maintained by Yokohama Minatomirai Railway, but the actual maintenance work is contracted to Tokyu Railways employees. Because Yokohama Minatomirai Railway does not own its own rail yard, trains are parked overnight at Tokyu Railways' Motosumiyoshi Rail Yard and at Motomachi-Chūkagai Station. There are plans to construct a portion of track for parking additional trains underneath Harbor View Park starting in 2020.

The Minatomirai Line is essentially an extension of the Tōkyū Tōyoko Line. The two lines operate as one, with no crew change at Yokohama station where trains cross between the two lines, in contrast to standard procedure with other line operators in Japan.

With the completion of the underground link line to the Tokyo Metro Fukutoshin Line on March 16, 2013, Minatomirai Line trains run onto the Fukutoshin Line via the Tōkyū Tōyoko Line and beyond to the Tōbu Tōjō Line, Seibu Yūrakuchō Line, and Seibu Ikebukuro Line. Along with the link to the Fukutoshin Line being established, Tōkyū Tōyoko and Minatomirai express trains (limited express/commuter limited express/express) were expanded from eight-car to ten-car configuration (with the exception of a portion of regular express trains). Platforms were extended at Minatomirai stations receiving express trains in order to be able to accommodate the extended ten-car configuration. Regular trains stopping at each station on the line continue to operate in the eight-car configuration.

All regular trains on the Minatomirai Line use the same services as the Tōyoko Line.

The S-train is the first service on the Minatomirai Line with fully reserved seating. On weekends and holidays it makes two and a half round trips (to Motomachi-Chūkagai Station twice and from the same station three times). All trains continue to the Seibu Ikebukuro Line, and one round trip begins and ends at the Seibu Chichibu Line's Seibu-Chichibu Station. Within the Minatomirai Line, these trains stop at Minatomirai Station and Motomachi-Chūkagai Station, but tickets are not sold for final destinations at these stations. S-train services use the Seibu 40000 series train exclusively.

Limited Express (特急, Tokkyū) trains run during daylight hours during the week and at all times excepting early morning and late night on weekends and holidays. The trains use 10 cars. Limited express trains stop at Yokohama Station, Minatomirai Station, and Motomachi-Chūkagai Station within the Minatomirai Line.

Commuter Limited Express (通勤特急, Tsūkin Tokkyū) operate during the morning rush hour and in the evening on weekdays. The trains use 10 cars and stop at all stations on the Minatomirai Line with the exception of Shin-Takashima Station. Many trains continue to the Fukutoshin Line via the Tōyoko Line as Commuter Express services.

Express (急行, Kyūkō) operate all day long. The trains stop at all stations on the Minatomirai Line with the exception of Shin-Takashima Station. Daytime trains use 8 cars, but 10 cars may be used during peak hours in the morning and evening.

Local (各駅停車, Kakueki-teisha) trains stop at all stations. Eight cars are used to align with the Tōkyū, Yokohama, and Tokyo Metro lines.