As of 2021, the INPR operated in two separate subdivisions, The Elgin Subdivision which operates from La Grande to Elgin (21.5 miles [34.6 km]) connecting at Elgin with another former UP rail line now owned by Wallowa County – which continues to Joseph, Oregon – and the Payette Subdivision Payette through Emmett and then into the canyon of the North Fork of the Payette River northward to Cascade.

This section, known as the Thunder Mountain Subdivision is considered the most scenic stretch of the INPR.

[1][2][3] In 1980 the Union Pacific abandoned the trackage from McCall to Cascade Idaho, In 1989 the UP put all four lines for sale as part of a package sale, this fell through and in 1993 these four lines were put up for sale, they were purchased by the Rio Grande Pacific Corporation in Texas who created the Idaho Northern and Pacific Railroad to operate the lines, in 1994 the INPR and UP reached an agreement to abandon the stretch of tracks from Nampa to Emmett, Idaho as it had been an increased fire risk in recent years, all interchanges now happened in Payette, in 1995 the INPR and UP reached an agreement to abandon the 85-mile (137 km) Weiser to Rubicon line and split the scrap money as the line had recently lost too much rail traffic to cover maintenance costs, in 1997 the mill in Joseph, Oregon closed and the INPR initiated abandonment paperwork, this however was prevented as the counties of Wallowa and Union, Oregon jointly bought the line from Elgin to Joseph to preserve it for future use, this line would later be used by the Wallowa Union Railroad to run the Eagle Cap excursion train.

However, the Boise Valley Railroad took over operation in 2009, possibly as a result of the post-housing boom recession.

[7][8] From 1998 until January 2016, the INPR operated the Thunder Mountain Line, a tourist railroad between Horseshoe Bend and Cascade.