The race was first held in 1966 as a standalone endurance event, one of three long-distance fixtures at Suzuka alongside the 500 km and the 12 Hours. These three races formed the Suzuka Circuit Endurance Series, which ran from 1967 to 1970. The event was suspended between 1974 and 1979 in response to the global oil crisis, returning in 1980 as a non-championship race held in the fourth weekend of August, a slot it would largely retain for decades.
From 1983 to 1991 the race was a round of the All Japan Endurance Championship, renamed the All Japan Sports Prototype Championship in 1987. The FIA World Sportscar Championship adopted the race in 1992, but the series collapsed after that season, leaving the 1993 running without championship status.
In 1994 the Suzuka 1000 km joined the inaugural BPR Global GT Series calendar, with Pokka becoming title sponsor. The race continued as a championship round through the BPR era and its successor the FIA GT Championship until 1999, when it reverted to non-championship status. During the early 2000s the event was open to Super GT and Super Taikyu machinery alongside clubman-class cars from Suzuka's own programs.
From 2006 the race became part of the Autobacs Super GT Series, where it stood as the longest and highest-points-paying event on the calendar. The Great Recession forced a reduction to 700 kilometres in 2009 and 2010, when it was renamed the Pokka GT Summer Special. The 2011 Tohoku earthquake and tsunami shortened the event further to 500 kilometres. The original 1,000-kilometre distance was restored from 2012.
Among drivers, Kunimitsu Takahashi holds the all-time record with four overall victories. Porsche leads the manufacturer standings with eleven wins spanning 1967 to 1994. Honda and Toyota have each won the race eight times overall, with Nissan recording seven victories. Eleven winners of the Suzuka 1000 km have also won the 24 Hours of Le Mans, including Henri Pescarolo, Vern Schuppan, André Lotterer, and Kazuki Nakajima.
In March 2017 the GT Association and the Stéphane Ratel Organisation announced a joint ten-hour format for the race using FIA-GT3 and JAF-GT300 cars, branded as the Suzuka 10 Hours. The reformatted event entered the Intercontinental GT Challenge in 2018 as the series' Asian round, replacing the Sepang 12 Hours. A prize purse of 100 million yen — 30 million to the outright winner — attracted the leading international GT3 factory operations alongside domestic Super GT teams. Two-time Formula One world champion Mika Häkkinen competed in the 2019 edition.
The 2020 and 2021 editions were cancelled due to the COVID-19 pandemic and Japanese travel restrictions. Suzuka's IGTC slot was temporarily filled by the Gulf 12 Hours at Yas Marina Circuit in 2022 and 2023.
During the 2024 SRO press conference at Spa-Francorchamps, Stéphane Ratel announced the race's return to the Intercontinental GT Challenge in 2025 under the revived Suzuka 1000 km name. Held on 14 September 2025, the event retained a timed format of six hours and 30 minutes — sufficient for the GT3 field to cover 1,000 kilometres — and included GT300-specification entries following an agreement between SRO and the GT Association.