Many functional diseases are related to dysautonomia, and heart rate variability has been used to assess dysautonomia. However, heart rate variability has not been studied in Spleen-Qi deficiency syndrome (SQDS). Healthy volunteers (n = 37) and patients with SQDS (n = 67), recruited from the Clinic of the State University of Ecatepec Valley were included in the study. Outcome measures were average heart rate, standard deviation of the normal-to-normal heartbeat intervals, low frequency (LF), high frequency (HF) power, and the LF/HF ratio. Also, intestinal peristalsis, gastrointestinal symptoms (GSs), fatigue, and level of attention were measured. Standard deviation of the normal-to-normal heartbeat intervals (17 ± 2.3%) and HF (14 ± 3.1%) were lower in SQDS patients (17 ± 1.3%) than in healthy volunteers. SQDS patients had higher heart rate, LF power, LF/HF ratio, and fatigue scores (9.6 ± 1.12%, 16 ± 2.1%, 22 ± 3.8%, and 21 ± 4.1%). The fatigue correlated positively with the LF/HF ratio and negatively with HF power. The SQDS group had lower concentration performance (16.2 ± 1.9%) in the d2 test. The intestinal peristalsis showed a reduction (15 ± 1.3%) as compared with control. GS score and peristalsis correlated negatively with HF. Our results suggest that the pathology of SDQS could be associated with a low vagal tone which causes a decrease in peristalsis, increased fatigue, reduced attention, and appearance of GSs.