On 19 November 2016, JR Hokkaido's President announced plans to rationalise the network by up to 1,237 km, or ~50% of the current network, including proposed conversion of the Naroyo - Wakkanai section of the Soya Line to Third Sector operation, but if local governments are not agreeable, the section will face closure.
Two Super Sōya limited express services each way operate between Sapporo and Wakkanai daily, and one Sarobetsu service each way also operates between Sapporo and Wakkanai daily. The latter service does not include Green car (first class) accommodation.
All-stations "Local" train services operate between Asahikawa and Nayoro, at approximately 1 to 2 hour intervals. All-stations "Local" train services operate between Nayoro and Wakkanai, at approximately 3 to 4 hour intervals. Four Nayoro Rapid services operate in each direction daily.
The line was originally built as part of a link between mainland Japan and the then Japanese northern frontier of Karafuto (southern half of Sakhalin Island). From Wakkanai Port, a ferry to then Ōdomari (present Korsakov) operated until the end of World War II.
The first segment of the line from Asahigawa (present Asahikawa) to Nagayama was built by the Hokkaido Government Railway in 1898. The line was extended to Nayoro in 1903, and to Wakkanai in 1922 along the route of the later Tempoku Line (天北線, Tenpoku-sen) via Hamatombetsu. The present route via Horonobe was opened as part of the Teshio Line (天塩線, Teshio-sen).
After Japan's defeat in the war, the line lost its function as a link to Sakhalin, but remained important as a trunk line into the northern part of Hokkaido. The Sōya Main Line gradually lost all of its branch lines, and presently constitutes a long branch from the Hakodate Main Line.
- A 138 km line known as the Nayoro Main Line was built from Nayoro to Engaru on the Sekihoku Main Line between 1915-1921, operating until 1989. There were four lines connecting to the Nayoro Main line: