This study aimed to objectively evaluate autonomic nervous function in children with primary Raynaud's phenomenon (PRP). Thirty-two children with PRP and 30 healthy subjects were included in the study. We analyzed heart rate variability (HRV) in the time domain by the following six standard time-domain measures: standard deviation of all normal R-R intervals during 24 h (SDNN), standard deviation of all normal R-R intervals for all 5-min segments (SDNNi), standard deviation of the average normal R-R intervals for all 5-min segments (SDANN), root mean square of the successive normal R-R interval difference, percentage of successive normal R-R intervals longer than 50 ms, and triangular index (integral of the density distribution of NN intervals divided by the maximum of the density distribution). The mean heart rate throughout 24 h was significantly higher in the PRP group than in the control group (p = 0.001). Although heart rate during the activity period was not significantly different from that during the night period, it was higher in the PRP group than in the control group (p = 0.002). In children with PRP, HRV analysis showed significantly lower values of SDNN (p = 0.01), SDNNi (p = 0.005), SDANN (p = 0.02), and HRV triangular index (p = 0.02) compared with the control group. HRV analysis for sympathovagal balance demonstrated a preponderance for the sympathetic component in patients with PRP. We conclude that all time-domain parameters evaluated in HRV analysis are significantly lower in children with PRP than in healthy subjects.