The 1999 Formula Nippon Championship was the twenty-seventh season of premier Japanese single-seater racing, and the fourth under the Formula Nippon name and Japan Race Promotion (JRP) management. The series was contested over ten rounds at five venues. 14 different teams, 26 different drivers, and three different chassis suppliers competed in the championship. Nakajima Racing driver Tom Coronel won the championship in his second season.
The series introduced the Exciting Point championship in 1999, which awarded points to drivers for setting the fastest laps of the race, running in the top six at each quarter of the race, and improving position throughout the race.
All teams used tyres supplied by Bridgestone and Mugen MF308 engines.
All races were held in Japan.