A method embodiment comprises generating a neural stimulation signal for a neural stimulation therapy. The signal is generated during a duty cycle of a stimulation period to provide the neural stimulation therapy with an intensity at a therapy level for a portion of the duty cycle. In various embodiments, a ramp up protocol is implemented to begin the duty cycle, a ramp down protocol is implemented to end the duty cycle, or both the ramp up protocol and the ramp down protocol are implemented. The ramp up protocol includes ramping up the intensity from a non-zero first subthreshold level for the neural stimulation therapy at the beginning of the duty cycle to the therapy level. The ramp down protocol includes ramping down the intensity from the therapy intensity level to a non-zero second subthreshold level for the neural stimulation therapy at the end of the duty cycle.