The purpose of this research was to investigate whether a decrement in self-control resources caused burnout among employees with different degrees of autonomy. We conducted a panel survey among 424 employees. The results revealed that 1) autonomy affected the relationship between controlling emotional sensations and burnout. Controlling emotional sensations increased burnout among employees with low autonomy, but not among those with high autonomy. Moreover, the results revealed that 2) autonomy did not affect the relationship between other self-control behaviors and burnout. We discussed why a decrement in self-control resources caused burnout and how autonomy affected it, by referring to the process of self-control based on the Limited Resource Model, cognitive control, and physiological underpinnings.