Shikoku Railway Company

At founding, the company's only profitable route — counting rail and bus together — was the Matsuyama–Kōchi express bus line. Change came quickly: the Sakaide–Tadotsu section of the Yosan Main Line was electrified on 2 October 1987; the Nakamura Line passed to the Tosa Kuroshio Railway in April 1988; and on 10 April 1988 the Honshi-Bisan Line opened across the Great Seto Bridge, linking Shikoku's rail network with Okayama on Honshu. The Marine Liner rapid service began that day, and the Uko railway ferry (its high-speed boats, suspended in 1990, were formally abolished in March 1991) was abolished as of the previous day. In June 1988 it stopped classifying lines as main, secondary or branch lines, unlike the other JR companies. The bridge lifted revenues, but highway-bus competition to the Keihanshin region intensified after the Akashi Kaikyō Bridge opened; in January 1996 the three JR 'island companies' fare revision ended the uniform nationwide JR fare structure.

Faced with the rapid construction of expressways across Shikoku, JR Shikoku pursued an aggressive programme of acceleration and modernization. In March 1989 it introduced the 2000 series — the world's first tilting (pendulum-type) diesel multiple unit — on the Nanpū and Shimanto limited expresses, while upgrades from 1988 raised line speeds in stages to 110–130 km/h. Yosan Line electrification, staged from 1990, was completed between Takamatsu and Iyoshi on 18 March 1993, and the 8000 series EMUs of 1992 took most of the Matsuyama-terminating Shiokaze and Ishizuchi services to 130 km/h; automatic signalling and CTC covered the whole network from November 1991. The Sunrise Seto sleeper between Tokyo and Takamatsu began in July 1998; in March 1999, with the Yoshino-gawa's withdrawal, JR Shikoku became the first of the six JR passenger companies to abolish kyūkō expresses entirely. On 1 March 2006 it became the first JR company to introduce station numbering, and in August 2019, when the last 113 series sets were retired, its entire revenue electric-train fleet became VVVF-inverter controlled, a JR Group first.

The railway business itself has run at a loss ever since the company was founded. As one of the three island companies, JR Shikoku received a management stabilization fund of 208.2 billion yen, whose interest offsets its operating deficit, supplemented by JRTT support and relief from fixed-asset taxes. In June 2011, under an amended law on former JNR debts, the scheme was reinforced: 140 billion yen was lent interest-free to purchase JRTT bonds paying a fixed 2.5 per cent for ten years (about 3.5 billion yen a year), plus 40 billion yen in grants and interest-free loans for renewing aging equipment. Ridership has nonetheless kept falling: usage in fiscal 2018 was about 30 per cent below fiscal 1988, expressway toll discounts bit deeply — rail income in fiscal 2009 fell 10.3 per cent, the largest drop since the company's founding, with about 2.3 billion yen of it attributed to the discounts — and in the year to March 2021 the COVID-19 pandemic produced an ordinary loss of 10.8 billion yen, the worst in the company's history. On 20 May 2023 fares were raised by an average of 12.82 per cent.

Recent decades have leaned on tourism and new sales channels. The Iyonada Monogatari, Shikoku's first full-scale sightseeing train, began on the Yosan Line in July 2014, followed by the Shikoku Mannaka Sennen Monogatari on the Dosan Line in 2017. Rather than issue its own IC fare card, JR Shikoku adopted JR West's ICOCA — at Takamatsu and Sakaide in 2012, between Takamatsu and Tadotsu and on the Seto-Ōhashi Line from March 2014, and at twenty stations from March 2020 — and in November 2022 launched the smartphone ticketing app 'Shikoku Smart Ekichan'. In March 2022 a joint management plan with Tokushima Bus in southern Tokushima Prefecture was approved — Japan's first joint management between a railway and a bus operator; in November 2020 the Mugi Line's Awa-Kainan–Kaifu section had been incorporated into the Asa Kaigan Railway's Asatō Line. Since the Hokkaido Shinkansen's partial opening it has been the only JR passenger company without a Shinkansen of its own, and — uniquely among all seven JR Group companies — it has had no fatal accident attributable to the company since founding. In December 2025 it completed the 3600 series hybrid local railcar.

• 19871 April: Upon the division and privatization of the Japanese National Railways (JNR), the Shikoku Railway Company (JR Shikoku) was formed, taking over the passenger railway operations of JNR's Shikoku General Bureau.
• 19872 October: The Sakaide–Tadotsu section of the Yosan Main Line was electrified.
• 198810 April: The Honshi-Bisan Line (Seto-Ōhashi Line) opened across the Great Seto Bridge and the Marine Liner rapid service began; the Uko ferry (excluding its high-speed boats) was abolished as of the previous day, 9 April.
• 198911 March: The 2000 series, the world's first tilting (pendulum-type) diesel multiple unit, entered service on the Nanpū and Shimanto limited expresses.
• 199215 August: The 8000 series electric multiple unit entered service on the Ishizuchi and Shiokaze limited expresses.
• 199318 March: With the electrification of the Imabari–Niihama section, electrification between Takamatsu and Iyoshi was completed; most Ishizuchi and Shiokaze services turning back at Matsuyama were switched to electric trains, and the maximum speed rose to 130 km/h.
• 199810 July: The Sunrise Seto overnight sleeper limited express linking Takamatsu with Tokyo began operating.
• 199913 March: With the withdrawal of the Yoshino-gawa service, JR Shikoku became the first of the six JR passenger companies to abolish kyūkō express trains entirely.
• 20041 April: The bus division was spun off as the subsidiary JR Shikoku Bus.
• 20061 March: Station numbering was introduced at all stations except temporary stations — the first such system among the six JR passenger companies — implemented jointly with the Tosa Kuroshio Railway and the Asa Kaigan Railway.
• 20141 March: ICOCA card service began between Takamatsu and Tadotsu on the Yosan Line and between Kojima and Utazu on the Honshi-Bisan (Seto-Ōhashi) Line, with the Shikoku-area 'SHIKOKU ICOCA' card issued in place of a proprietary IC card.
• 201426 July: Shikoku's first full-scale sightseeing train, the Iyonada Monogatari, began operating on the Yosan Line.
• 20201 November: The Awa-Kainan–Kaifu section of the Mugi Line was incorporated into the Asa Kaigan Railway's Asatō Line.
• 2022March: The 'joint management plan for southern Tokushima Prefecture' between JR Shikoku and Tokushima Bus was approved by the Minister of Land, Infrastructure, Transport and Tourism under the special act on exemptions from the Antimonopoly Act — the first joint management between a railway and a bus operator in Japan; in November the smartphone ticketing app 'Shikoku Smart Ekichan' entered service (24 November).