Previous findings of time-of-day differences in athletic performance could be confounded by diurnal fluctuations in environmental and behavioral “masking” factors (e.g., sleep, ambient temperature, and energy intake). The purpose of this study was to examine whether there is a circadian rhythm in swim performance that is independent of these masking factors. Experienced swimmers (n = 25) were assessed for 50–55 consecutive hours in the laboratory. The swimmers followed a 3-h “ultra-short” sleep-wake cycle, involving 1 h of sleep in darkness and 2 h of wakefulness in dim light, that was repeated throughout the observation. The protocol distributes behavioral and environmental masking factors equally across the 24-h period. Each swimmer was scheduled to perform six maximal-effort 200-m swim trials that were distributed equally across eight times of day (n = 147 trials). Each trial was separated by 9 h. A cosine fit of intra-aural temperature data established the time of the lowest body temperature (T_min). Swim performances were z-transformed and compared across the eight times of day and across twelve 2-h intervals relative to T_min. Analysis of covariance, controlling for trial number, revealed a significant (P < 0.001) pattern in swim performance relative to environmental and circadian times of day. Performance peaked 5–7 h before T_min (∼2300) and was worst from 1 h before to 1 h after T_min (∼0500). Mean swim performance was 169.5 s; circadian variation from peak to worst performance was 5.8 s. These data suggest a circadian rhythm in athletic performance independent of environmental and behavioral masking effects.