Acute low back pain (ALBP) is often associated with altered autonomic balance and elevated sympathetic activity, contributing to increased pain perception and delayed recovery. This study aimed to investigate the effects of electrical acupuncture pen therapy (EAPT) on heart rate variability (HRV) and autonomic function in patients with ALBP. A total of 60 participants (aged 25–55 years) with clinically diagnosed ALBP were randomly assigned to either the EAPT group (n = 30) or a sham-treatment control group (n = 30). The EAPT group received 20-minute sessions of electrical stimulation using a handheld acupuncture pen at standardized lumbar acupoints Results showed that the EAPT group demonstrated a significant increase in HF power (p < 0.01) and a reduction in LF/HF ratio (p < 0.05), indicating enhanced parasympathetic activity and improved autonomic balance compared to the control group. Moreover, VAS and ODI scores decreased significantly in the EAPT group (both p < 0.001), suggesting reduced pain intensity and better functional outcomes. No adverse effects were reported.