An apparatus and method for mapping timer channels to protection groups. One embodiment of the method can be implemented in a microcontroller unit (MCU) that comprises a central processing unit (CPU) coupled to a plurality of timer channels and a plurality of programmable group output disable (PTGOD) circuits. The CPU can select a first group of the timer channels to respond to an assertion of a first output disable signal from a first of the PTGOD circuits. Each timer channel of the first group can disable an output signal in response to receiving the assertion of the first output disable signal.