A system and method are provided for synchronizing a programmable timer time base and an external time signal. The method either accepts or supplies an external time signal (e.g., IEEE 1588) at an external interface, links a synchronized time base to the external time signal, and clocks a channel time base with the synchronized time base. Then, a timer channel can be used to perform programmable timer functions in response to the channel time base. Some programmable timer functions include input capture, output compare, quadrature decoding, pulse measurement, frequency measurement, and pulse width modulation (PWM) functions. In one aspect, accepting the external time signal at the external interface includes detecting a packet with a time value. In another aspect, the method uses the channel to detect an event at a channel external interface, and compares the channel time base counter value with an expected value to modify the synchronized time base.