The first Formula Three championship in Japan was established by the Nippon Formula 3 Association in 1979, with Toshio Suzuki taking victory in its inaugural running. By 1981 the series had grown into a fully national-level championship organised by the Japan Automobile Federation (JAF).
Foreign drivers began participating with increasing frequency through the 1980s, and by the early 1990s international competitors had come to dominate the championship's results. This international character distinguished the Japanese Formula 3 Championship from purely domestic series and helped raise its global profile.
In 2008 the series adopted a two-tier structure to broaden participation. The upper Championship class was open to cars conforming to the current three-year equipment cycle, while a lower National class accepted cars from the previous cycle using a specification Toyota engine. This format remained in place for much of the series' latter years.
The series permitted competitors to use any eligible chassis conforming to the Formula Three technical regulations. From 2007 onward only Dallara chassis were used in practice, though earlier decades had seen a variety of manufacturers supply cars including March, Reynard, Ralt, and Japanese constructors TOM'S and Dome.
Engine supply was pluralistic throughout the series' history. Toyota-TOM'S, Mugen-Honda, Toda Racing, and ThreeBond (Nissan) were among the principal engine suppliers in the championship's later years. Previous suppliers had included Volkswagen, HKS (Mitsubishi), Fiat, and Opel. Tyre supply passed through several hands — Bridgestone, Dunlop, and Yokohama all provided rubber in the series' early years, before Bridgestone became sole supplier from 1988. Hankook held the sole supply contract in 2009 following the end of the Bridgestone arrangement.
Prior to the revision of FIA Super Licence requirements ahead of the 2016 Formula One season, the Japanese Formula 3 Championship was one of four major Formula Three championships worldwide whose champion automatically received an FIA Super Licence. Under the revised system introduced from 2016, the championship winner earned 10 points toward their Super Licence, with smaller allocations for drivers finishing second through fifth in the final standings.
As part of the FIA's restructuring of global Formula Three nomenclature, series promoter Japan Race Promotion announced on 13 August 2019 that the championship would be rebranded as Super Formula Lights. The FIA's new regulations prohibited regional series from using the designation "Formula 3" — that name was reserved for the European-based FIA Formula 3 Championship — and similarly prohibited the "Formula Regional" name, which was being adopted by other regional Formula Three competitions from 2020.
With the rebrand, the Japanese Formula 3 Championship officially concluded after 41 years of competition, having run from 1979 through 2019. The Japan Formula 3 Association continued to administer the successor Super Formula Lights series. Separately, the FIA awarded rights for a Formula Regional championship in Japan to K2, promoters of the F4 Japanese Championship, under the name Formula Regional Japanese Championship.
The Japanese Formula 3 Championship served as a launching pad for numerous drivers who went on to international careers. Its blend of domestic Japanese machinery, international entrants, and recognition as a Super Licence pathway gave it standing comparable to the leading Formula Three series in Europe. Super Formula Lights has continued in its footsteps as the principal feeder series for Super Formula, Japan's premier open-wheel category.