The purpose of this study was to investigate the effects of a short-term low- or high-carbohydrate (CHO) diet consumed after exercise on sympathetic nervous system activity. Twelve healthy males underwent a progressive incremental test; a control measurement of plasma catecholamines and heart rate variability (HRV); an exercise protocol to reduce endogenous CHO stores; a low- or high-CHO diet (counterbalanced order) consumed for 2 days, beginning immediately after the exercise protocol; and a second resting plasma catecholamine and HRV measurement. The exercise and diet protocols and the second round of measurements were performed again after a 1-week washout period. The mean (±SD) values of the standard deviation of R–R intervals were similar between conditions (control, 899.0 ± 146.1 ms; low-CHO diet, 876.8 ± 115.8 ms; and high-CHO diet, 878.7 ± 127.7 ms). The absolute high- and low-frequency (HF and LF, respectively) densities of the HRV power spectrum were also not different between conditions. However, normalized HF and LF (i.e., relative to the total power spectrum) were lower and higher, respectively, in the low-CHO diet than in the control diet (mean ± SD, 17 ± 9 normalized units (NU) and 83 ± 9 NU vs. 27 ± 11 NU and 73 ± 17 NU, respectively; p < 0.05). The LF/HF ratio was higher with the low-CHO diet than with the control diet (mean ± SD, 7.2 ± 6.2 and 4.2 ± 3.2, respectively; p < 0.05). The mean values of plasma catecholamines were not different between diets. These results suggest that the autonomic control of the heart rate was modified after a short-term low-CHO diet, but plasma catecholamine levels were not altered.