Before the opening of the Jōetsu Shinkansen in 1982, the Joetsu Line had frequent service by express trains connecting Tokyo and Niigata.

When completed, the line shortened the Ueno to Niigata route by 98 km (61 mi), and included two spiral sections in the tunnels.

Passengers catching Miyauchi-bound (northbound) trains at Yubiso and Doai stations do so from platforms situated underground within the Shin-Shimizu tunnel.

The 2004 Chūetsu earthquake seriously damaged the Jōetsu Line, closing the Minakami to Miyauchi section for about two months.

In late July 2011, torrential rainfall damage resulted in the closure of the Echigo-Yuzawa - Muikamachi section for two weeks.