The 1999 Toyota Atlantic Championship season was contested over 12 rounds.

The KOOL Toyota Atlantic Championship Drivers' Champion was Anthony Lazzaro driving for PPI Motorsports.

In this one-make formula all drivers had to utilize Swift chassis and Toyota engines.

This season also saw a C2-class running older Ralt chassis and Toyota engines.

Note: Race 8 Nicolas Rondet had 2 points deduction due to taking unjustifiable risk.