Circadian rhythms, among other factors, have been shown to regulate key physiological processes involved in athletic performance. Personal best performance of athletes in the evening was confirmed across different sports. Contrary to this view, we identified peak performance times in athletes to be different between human “larks” and “owls” (also called “morningness/eveningness types” or “chronotypes” and referred to as circadian phenotypes in this paper), i.e., individuals with well-documented genetic and physiological differences that result in disparities between their biological clocks and how they entrain to exogenous cues, such as the environmental light/dark cycle and social factors. We found time since entrained awakening to be the major predictor of peak performance times, rather than time of day, as well as significant individual performance variations as large as 26% in the course of a day. Our novel approach combining the use of an athlete-specific chronometric test, longitudinal circadian analysis, and physical performance tests to characterize relevant sleep/wake and performance parameters in athletes allows a comprehensive analysis of the link between the circadian system and diurnal performance variation. We establish that the evaluation of an athlete’s personal best performance requires consideration of circadian phenotype, performance evaluation at different times of day, and analysis of performance as a function of time since entrained awakening.