The adequate time to perform physical activity (PA) to maintain optimal circadian system health has not been defined. We studied the influence of morning and evening PA on circadian rhythmicity in 16 women with wrist temperature (WT). Participants performed controlled PA (45 min continuous-running) during 7 days in the morning (MPA) and evening (EPA) and results were compared with a no-exercise-week (C). EPA was characterized by a lower amplitude (evening: 0.028 ± 0.01 °C versus control: 0.038 ± 0.016 °C; p < 0.05) less pronounced second-harmonic (power) (evening: 0.41 ± 0.47 versus morning: 1.04 ± 0.59); and achrophase delay (evening: 06:35 ± 02:14 h versus morning: 04:51 ± 01:11 h; p < 0.05) as compared to MPA and C. Performing PA in the late evening might not be as beneficial as in the morning.