In addition, the Hisatsu Line (one morning train that stops at this station and returns to the station), and some trains that run directly to the Hisatsu Orange Railway Line (one daytime and two evening local trains bound for Izumi and one evening Orange Restaurant train that stops at this station and returns to the station) use the crossover toward Kagoshima from the upbound Kumamoto platform and return to Kagoshima.

A special elevated spur ran from north of the station to the Shinkansen platform from 2004 to 2011 and was used by Relay Tsubame limited express trains from Hakata on the Kagoshima Line provided the link to the Shinkansen line, and Shin-Yatsushiro was designed to facilitate an easy and fast connection between the Relay Tsubame train and the Tsubame shinkansen train on the same platform.

The spur line was not used by regular services, but was utilized in 2014 for reliability trials of the Gauge Change Train between Kumamoto and Kagoshima-Chuo Station, including gauge changing on the spur line.

[4] The trials were originally planned to run for three years starting in April 2014, but were suspended that December after defects were found in the train bogies.

On 8 November 2021, a man was arrested at the station after an attempted arson on board a Sakura service.