Studies have shown that alertness can affect inhibitory control, the mechanism responsible for stopping behaviors, thoughts, or emotions. Inhibitory control is particularly important for helping individuals with Obsessive–Compulsive Disorder (OCD) resisting their symptoms. Chronotype is the mechanism governing an individual’s fluctuation of alertness throughout the day. Previous studies have shown that individuals with a ‘morning’ chronotype have worse OCD symptoms in the evening and vice versa. We administered a novel ‘symptom-provocation stop signal task’ (SP-SST), in which individually tailored OCD triggers were presented and inhibitory control was measured. Twenty-five treatment-seeking OCD patients completed the SP-SST three times per day for seven consecutive days. Stop signal reaction time (SSRT), which measures inhibitory control, was calculated separately for symptom-provocation trials and for neutral trials. Results yielded that: (a) stopping was significantly harder in the symptom-provocation compared to neutral trials, and (b) the chronotype by time-of-day interaction predicts inhibition for both symptom-provocation and neutral trials, indicating better inhibition in the optimal time of day. Furthermore, we concluded that individually tailored OCD triggers have a detrimental effect on inhibitory control. Most importantly, higher alertness levels, which can be predicted by the interaction of chronotype and time of day, affect inhibitory control, both in general and for OCD triggers specifically.