The main purpose of this study was to compare the effect of the constant load and self-paced exercise with similar total work on autonomic control after endurance exercise. Ten physically active men were submitted to (i) a maximal incremental exercise test, (ii) a 4-km cycling time trial (4-km TT), and (iii) a constant workload test with identical total external work performed at 4-km TT. Gas exchange was measured throughout the tests, while blood lactate, heart rate, and heart rate variability (HRV) were measured during the passive recovery. Power output measured at the last lap (i.e. 3600-4000 m) of 4-km TT (316 +/- 89 W) was statistically higher than power output measured at the end of the constant workload exercise (211 +/- 42 W). The 4-km TT produced higher values of blood lactate concentration (8.8 +/- 2.1 mmol L(-1)) than the constant workload test (7.8 +/- 2.1 mmol L(-1)). The heart rate recovery measured at 60 s (constant workload: 37 +/- 7 bpm; 4-km TT: 30 +/- 6) and 120 s (constant workload: 57 +/- 9 bpm; 4-km TT: 51 +/- 9 bpm) were higher in the constant workload than in the self-paced exercise. The HRV (i.e. RMSSD30s) was statistically higher in the constant load exercise measured at 120, 420, 450, 480, 540, and 570 s than the self-paced exercise. These findings suggest that the autonomic control responses were dependent of the endurance exercise modalities, with parasympathetic activity being delayed after self-paced exercise, as evidenced by post-exercise heart rate indices.