It ran between the city of Sapporo on the northern island of Hokkaido and Osaka in south-western Honshu, a distance of approximately 1,500 km (930 mi), with the journey taking between 22 and 23 hours.

Trains for Sapporo departed Osaka at 12:00, calling at Shin-Osaka, Kyoto, Tsuruga, Fukui, Kanazawa, Takaoka, Toyama, Naoetsu, and Nagaoka, with the final passenger pick-up made at in then at Niitsu at 19:31.

The same stops were made in the reverse, with the Twilight Express departing Sapporo at 14:05 and making its final pickup at Tōya at 16:33.

The first stop at Niitsu was made at 04:33, with the train eventually making its way to Kyoto at 12:15 and finally arriving at Osaka at 12:52.

The Nihonkai train made daily round-trip runs between Osaka and Aomori, with ongoing connections to Sapporo.

[3] The view from inside the "royal suite" in car 8 was obstructed by the adjacent generator van.

[8] In April 1991, a third rake of coaches was introduced, allowing daily operations during busy seasons.

[2] In June 2017, JR West introduced a new luxury sleeping-car excursion train named Twilight Express Mizukaze, continuing the name and brand established by the Twilight Express train service.

[11] The Twilight Express formed the main backdrop for the TBS TV drama Terminus: Love on the Twilight Express (終着駅-トワイライトエクスプレスの恋), starring Kōichi Satō and Miho Nakayama, and broadcast on 20 March 2012.