The 1999 Japan Golf Tour was the 27th season of the Japan Golf Tour (formerly the PGA of Japan Tour), the main professional golf tour in Japan since it was formed in 1973.
It was the first season in which the newly formed Japan Golf Tour Organization took over the running of the tour, separating from the PGA of Japan.
The following table lists official events during the 1999 season.
The following events were sanctioned by the Japan Golf Tour, but did not carry official money, nor were wins official.
The money list was based on prize money won during the season, calculated in Japanese yen.
The 1999 Japan Challenge Tour was the 15th season of the Japan Challenge Tour, the official development tour to the Japan Golf Tour.
The following table lists official events during the 1999 season.
The money list was based on prize money won during the season, calculated in Japanese yen. The top five players on the money list earned status to play on the 2000 Japan Golf Tour (iiyama Tour).