Tokyo Metro Namboku Line through-running network

The completion to Meguro was also the moment the line became a through-running hub. On 26 September 2000, through-services began at the southern terminus, Meguro, onto the Tokyu Meguro Line, operated by Tokyu Corporation. This was the Namboku Line's first through-running partner, sending trains south through Tokyu's network. Less than half a year later, on 28 March 2001, the Saitama Rapid Railway Line opened and through-running began at the northern terminus, Akabane-Iwabuchi, carrying Namboku Line trains onward into Saitama Prefecture as far as Urawa-Misono. The Saitama Rapid Railway Line is in effect a northern extension of the Namboku Line, yet it is a separate operator to which the Namboku Line provides through-services; it notably handled traffic to and from Saitama Stadium during the 2002 World Cup.

A distinctive feature of the southern end is that the right-of-way and stations between Shirokane-Takanawa and Meguro are shared with the Toei Mita Line, an arrangement in which two operators share common infrastructure. Both the Namboku Line and the Mita Line through-run onto the Tokyu Meguro Line from this shared section.

The through-running corridor was progressively lengthened to the south. On 22 June 2008, when the Tokyu Meguro Line was extended from Musashi-Kosugi to Hiyoshi, Namboku Line through-services followed to Hiyoshi. The most significant southern expansion came with the timetable revision of 18 March 2023: the newly opened Tokyu Shin-Yokohama Line and Sotetsu Shin-Yokohama Line allowed through-services to continue beyond Hiyoshi onto the Sagami Railway (Sotetsu) network. Most southbound trains past Hiyoshi now run as far as Shin-Yokohama, with services continuing toward Ebina on the Sotetsu Main Line and Shonandai on the Sotetsu Izumino Line.

The Namboku Line was inherited by Tokyo Metro in 2004 following the privatisation of the Teito Rapid Transit Authority. In its rolling-stock pool the through-running arrangement is reflected by trains from each partner operating across the network: Tokyo Metro's own 9000 series alongside Saitama Rapid Railway, Tokyu and Sotetsu stock. From a single isolated segment in 1991, the line has grown into the spine of a corridor that, by 2023, connected the Saitama suburbs in the north with the Sotetsu network around Yokohama in the south.

Through-services run across operator boundaries during regular daytime operation. At the northern terminus, Akabane-Iwabuchi, trains run through onto the Saitama Rapid Railway Line toward Urawa-Misono. At the southern terminus, Meguro, trains run through onto the Tokyu Meguro Line toward Hiyoshi, and since 18 March 2023 most services past Hiyoshi continue via the Tokyu and Sotetsu Shin-Yokohama Lines to Shin-Yokohama, with onward running toward Ebina (Sotetsu Main Line) and Shonandai (Sotetsu Izumino Line). The Shirokane-Takanawa to Meguro section is shared with the Toei Mita Line, whose trains also through-run onto the Tokyu Meguro Line.

• 1991The Namboku Line opened its first segment, Komagome to Akabane-Iwabuchi (6.3 km), on 29 November 1991, initially running four-car trains. At this stage the line operated on its own, with no through-running partners.
• 2000On 26 September 2000 the final segment from Tameike-Sanno to Meguro opened, completing the full line, and through-running with the Tokyu Meguro Line began at Meguro — the first through-service partner of the Namboku Line.
• 2001On 28 March 2001 the Saitama Rapid Railway Line opened and through-running began at Akabane-Iwabuchi, extending services northward into Saitama as far as Urawa-Misono. The Saitama line functions in effect as a northern extension of the Namboku Line but remains a separate operator.
• 2008On 22 June 2008, following the Tokyu Meguro Line's extension from Musashi-Kosugi to Hiyoshi, Namboku Line through-services were extended south to Hiyoshi.
• 2023Effective the timetable revision of 18 March 2023, through-running was extended beyond Hiyoshi onto the new Tokyu Shin-Yokohama Line and the Sotetsu Shin-Yokohama Line, reaching the Sagami Railway (Sotetsu) network. Most southbound services past Hiyoshi continue to Shin-Yokohama and on toward Ebina on the Sotetsu Main Line and Shonandai on the Sotetsu Izumino Line.