Heart rate (HR) recovery (HRR) and variability (HRV) after exercise are non-invasive tools used to assess cardiac autonomic regulation and cardiovascular prognosis. Autonomic recovery is slower after evening than morning exercise in healthy individuals, but this influence is unknown in subjects with autonomic dysfunction, although it may affect prognostic evaluation. This study compared post-exercise HRR and HRV after maximal morning and evening exercise in pre-hypertensive men. Ten volunteers randomly underwent two maximal exercise tests conducted in the morning (8-10 a.m.) and evening (6-8 p.m.). HRR60s (HR reduction at 60 s of recovery - prognostic index), T30 (short-term time-constant of HRR - parasympathetic reactivation marker), rMSSD30s (square root of the mean of the sum of the squares of differences between adjacent R-R intervals on subsequent 30 s segments - parasympathetic reactivation marker), and HRRτ (time constant of the first order exponential fitting of HRR - marker of sympathetic withdraw and parasympathetic reactivation) were measured. Paired t-test and two-way ANOVA were used. HRR60s and HRRτ were similar after exercise in the morning and evening (27 ± 7 vs. 29 ± 7 bpm, p = 0.111, and 79 ± 14 vs. 96 ± 29 s, p = 0.119, respectively). T30 was significantly greater after evening exercise (405 ± 215 vs. 295 ± 119 s, p = 0.002) and rMSSD30s was lower in the evening (main factor session, p = 0.009). In conclusion, in pre-hypertensive men, the prognostic index of HRR, HRR60s, is not affected by the time of day when exercise is conducted. However, post-exercise parasympathetic reactivation, evaluated by T30 and rMSSD30s, is blunted after evening exercise.