Pain intensity has been reported to fluctuate during the day in some experimental and clinical conditions, but the mechanisms underlying these fluctuations are unknown. Although the circadian timing system is known to regulate a wide range of physiological functions, its implication in pain regulation is unknown. Using highly controlled laboratory constant routine conditions, we show that pain sensitivity is rhythmic over the 24-hours and strongly controlled by the endogenous circadian timing system. We found that the circadian component of pain sensitivity can be modelled with a sinusoidal function, with a maximum in the middle of the night and a minimum in the afternoon. We also found a weak homeostatic control of pain sensitivity, with a linear increase over the 34 hours of prolonged wakefulness, which slowly builds up with sleep pressure. Using mathematical modelling, we describe that the circadian system accounts for ~80% of the full magnitude of pain sensitivity over the 24 hours, and that sleep-related processes account for only ~20%. Overall, our data reveal that the neurobiological mechanisms involved in driving the rhythmicity of pain perception in humans, with the oscillating time-piece located in the suprachiasmatic nuclei. Our findings highlight the need to consider the time of day in pain assessment, and suggest that personalized circadian medicine may be a promising approach to pain management.