A protection circuit for a multiple output switching mode power converter protects against an over-current or short circuit failure condition. The protection circuit activates the soft-start circuit of the PWM control circuit upon detection of the over-current or short circuit condition. The soft-start circuit then shuts off operation of the power converter and restarts the power converter after a period of time defined by the soft-start circuit. The protection circuit is effective with any type of power converter topology (e.g., buck, boost, flyback, and forward converter), isolated or non-isolated, having dual or multiple outputs.