In 1996, Team Goh of Japan purchased two F1 GTRs of 1996-spec, chassis #13R and #14R, for participation in the All Japan Grand Touring Car Championship's (JGTC) GT500 class under the name Team Lark. Debuting at the opening round at Suzuka Circuit, the Lark team took a 1-2 finish, with winners Naoki Hattori and Ralf Schumacher. At the following round at Fuji, David Brabham and John Nielsen would take victory for the Lark McLaren. However, in the next two rounds, the Japanese rivals would overcome the McLarens, only to have Team Lark return to take victory in the final two rounds of the season. At the Sugo round, Lark badly damaged their one chassis, requiring them to borrow chassis #04R from GTC Competition as a replacement for the final JGTC round. With four victories on the season, Team Lark captured the GT500 teams championship ahead of factory squads from Toyota and Nissan. Team Lark's championship victory was the second season in JGTC/Super GT history where the GT500 class-winning car is not from a Japanese manufacturer; a Porsche 911 GT2 won the GT500 team's championship in 1995, although the driver championship was won by a Nissan driver that year.
Team Lark would not return to defend their title in 1997 due to disputes with GT Association over car handicaps, and no McLarens raced in the series. McLarens would return though in 1999 with Team Take One purchasing McLaren F1 GTR #19R, a 1997-spec car, for competition in GT500. The competition from Toyota, Honda, and Nissan had improved since the McLaren last raced, and therefore Team Take One struggled to be competitive, achieving only a best 9th place at Mine Circuit.
For 2000, Hitotsuyama Racing decided to follow Team Take One's lead and enter their own 1997-spec chassis, #25R, which the team had previously used in the 1999 Le Mans Fuji 1000km. Although both teams suffered mechanical woes throughout the season, Team Take One was able to take a fourth-place finish at TI Aida. Both teams continued into 2001, with the Take One McLaren outperforming the Hitotsuyama entry in most rounds. However a shock occurrence happened at the end of the season when the Take One McLaren was able to secure overall victory at Mine Circuit, a mere nine seconds ahead of a factory Nissan Skyline GT-R, and helping boost Team Take One to 8th in the teams championship.