Hokkaido Railway Company

The first decade reshaped that inheritance. On 13 March 1988 the Kaikyō Line through the Seikan Tunnel opened and regular sailings of the Seikan ferry ended the same day; the route was formally abolished that September after a brief revival. Deficit-ridden local lines closed in succession — Horonai (1987), Matsumae and Utashinai (1988), Shibetsu, Nayoro Main and Tempoku (1989) — and the Chihoku Line was converted to the Hokkaidō Chihoku Kōgen Railway in June 1989. In January 1996 the three JR 'island companies' revised their fares, breaking the uniform nationwide JR fare structure; the bus business passed to subsidiary JR Hokkaido Bus in April 2000, and the Kitaca smart card was introduced in the Sapporo area on 25 October 2008.

JR Hokkaido's economics have been precarious from the outset. One of the three JR 'island companies' expected to struggle even before the JNR breakup, it received a management stabilization fund with a principal of 682.2 billion yen, whose investment returns were to cover its operating shortfall. After the bubble economy collapsed, interest rates fell far below the levels assumed at founding and the returns shrank. Most of its network crosses sparsely populated country, road and air competition is intense, and the snowy, cold service area imposes large maintenance costs. In March 2021 an amendment to the law on disposing of former JNR liabilities made continued state support possible through fiscal 2030, with 130.2 billion yen announced for the following three years.

Years of cost-cutting under chronic deficits were followed by a series of safety failures. On 27 May 2011 the Super Ōzora 14 limited express derailed and caught fire inside a Sekishō Line tunnel in Shimukappu, burning out six cars, and the company received a business improvement order that June. On 19 September 2013 a freight train derailed at Ōnuma Station on the Hakodate Main Line and the investigation revealed falsified rail-inspection data; in February 2014 the transport ministry (MLIT) filed a criminal accusation against the company under the Railway Business Act. In January 2014 the transport minister issued a business improvement order and a supervisory order, with 60 billion yen of capital-investment support from JRTT, followed by accelerated track repairs and rolling-stock replacement. After further lapses, in May 2025 JR Hokkaido became the first railway in Japan placed under MLIT's 'strengthened safety audit system'.

On 26 March 2016 the Hokkaido Shinkansen opened between Shin-Aomori and Shin-Hakodate-Hokuto (148.9 km), with H5 series trains running through to JR East's Tohoku Shinkansen; the Esashi Line between Goryōkaku and Kikonai passed to the South Hokkaido Railway the same day. The overnight and through trains across the tunnel — Hokutosei, Cassiopeia, Hakuchō, Super Hakuchō, Hamanasu — ended in 2015–2016, leaving the Shinkansen as the company's only regular passenger link to Honshu. In March 2019 the tunnel's maximum speed was raised to 160 km/h, cutting the fastest Tokyo–Shin-Hakodate-Hokuto time to 3 hours 58 minutes. The 211.3 km extension to Sapporo is under construction, scheduled (as of October 2025) to open in 2038.

On 16 November 2016 President Shimada announced that about 1,237 km — roughly half of the then network of just over 2,500 km — could not be maintained by JR Hokkaido alone, across thirteen sections to be bus-converted or locally supported. Closures followed in stages: Rumoi Main Line Rumoi–Mashike (December 2016), the Yūbari branch of the Sekishō Line (April 2019), the Sasshō Line beyond Hokkaidō-Iryōdaigaku (2020), the Hidaka Main Line beyond Mukawa (April 2021), Ishikari-Numata–Rumoi (April 2023), Nemuro Main Line Furano–Shintoku (April 2024) and finally Fukagawa–Ishikari-Numata on 1 April 2026, completing the closure of all five sections marked for abolition in 2016. On 15 April 2026 President Watanuki proposed vertical separation for the eight remaining difficult sections, with JR Hokkaido running trains while local-government entities own the track and facilities. As of 1 April 2026 the network comprises thirteen lines totalling 2,240.5 operating kilometres: six trunk lines (1,378.9 km, including the Shinkansen) and seven regional lines (861.6 km).

• 19871 April: Upon the division and privatization of the Japanese National Railways (JNR), the Hokkaido Railway Company (JR Hokkaido) was formed, inheriting 21 railway lines totalling 3,176.6 km, a 113.0 km ferry route and a bus business.
• 198813 March: The Kaikyō Line through the Seikan Tunnel opened and regular Seikan ferry sailings ended the same day; after a temporary revival the ferry route was formally abolished on 19 September 1988.
• 19894 June: The Chihoku Line (Ikeda–Kitami) was abolished and converted to the Hokkaidō Chihoku Kōgen Railway.
• 199610 January: JR Hokkaido and the other two JR 'island companies' revised their fares, ending the uniform nationwide JR fare structure that had continued from the JNR era.
• 20001 April: The bus business was transferred to the wholly owned subsidiary JR Hokkaido Bus.
• 200825 October: The Kitaca contactless smart card was introduced in the Sapporo area.
• 201127 May: The Super Ōzora 14 limited express derailed and caught fire inside the 1st Niniu Tunnel on the Sekishō Line in Shimukappu, burning out six cars; on 18 June the company received a business improvement order from MLIT.
• 201319 September: A freight train derailed at Ōnuma Station on the Hakodate Main Line; the investigation revealed that rail inspection data had been falsified.
• 2014January: The Minister of Land, Infrastructure, Transport and Tourism issued JR Hokkaido a business improvement order and a supervisory order on transport safety and the sound operation of the business, accompanied by 60 billion yen of capital-investment support from the Japan Railway Construction, Transport and Technology Agency.
• 201626 March: The Hokkaido Shinkansen opened between Shin-Aomori and Shin-Hakodate-Hokuto, with H5 series trains running through onto JR East's Tohoku Shinkansen; the Esashi Line between Goryōkaku and Kikonai was transferred to the South Hokkaido Railway the same day.
• 201616 November: President Shimada and other executives announced that about 1,237 km — roughly half of the then network of just over 2,500 km — could not be maintained by JR Hokkaido alone, identifying thirteen sections for bus conversion or local financial support.
• 20207 May: The Sasshō Line between Hokkaidō-Iryōdaigaku and Shin-Totsukawa (47.6 km) was formally abolished; the final trains had run on 17 April 2020, brought forward because of the COVID-19 pandemic.
• 20241 April: The Nemuro Main Line between Furano and Shintoku (81.7 km) was abolished.
• 20261 April: The Rumoi Main Line between Fukagawa and Ishikari-Numata was abolished, completing the closure of all five sections JR Hokkaido had marked for abolition in 2016; on 15 April President Watanuki proposed a vertical-separation scheme for the eight remaining difficult-to-maintain sections, with entities formed by local governments owning the infrastructure while JR Hokkaido continues to operate the trains.