The purpose of the present study was to examine the effects of active warm-up duration on the diurnal fluctuations in anaerobic performances. Twelve physical education students performed a medical stress test (progressive test up to exhaustion) and four Wingate tests (measurement of peak power [P(peak)], mean power [P(mean)], and fatigue index during an all-out 30 s cycling exercise). The tests were performed in separate sessions (minimum interval = 36 h) in a balanced and randomized design at 08:00 and 18:00 h, either after a 5 min (5-AWU) or a 15 min active warm-up (15-AWU). AWU consisted of pedaling at 50% of the power output at the last stage of the stress exhausting test. Rectal temperature was collected throughout the sessions. A two-way ANOVA (warm-up x time of day) revealed a significant interaction for P(peak) (F((1.11)) = 6.48, p < 0.05) and P(mean) (F((1.11)) = 5.84, p < 0.05): the time-of-day effect was significant (p < 0.001) in contrast with the effect of warm-up duration (p > 0.05). P(peak) and P(mean) improved significantly from morning to afternoon after both 5-AWU and 15-AWU, but the effect of warm-up duration was significant in the morning only. Indeed, the values of P(peak) or P(mean) were the same after both warm-up protocols in the afternoon. For rectal temperature, there was no interaction between time-of-day and warm-up duration. Rectal temperature before and after both the warm-up protocols was higher in the afternoon, and the effect of warm-up duration on temperature was similar at 08:00 and 18:00 h. In conclusion, the interpretation of the results of the anaerobic performance tests should take into account time-of-day and warm-up procedures. Longer warm-up protocols are recommended in the morning to minimize the diurnal fluctuations of anaerobic performances.