Heart rate variability (HRV) analysis has emerged as a simple and non-invasive technique to indirectly evaluate the autonomic nervous system (ANS), and it is considered a sensible and advanced index of health status. Pulsed electromagnetic fields (PEMFs) are widely used in clinical settings for improving the health status of individuals with chronic musculoskeletal pain. The aim of the present single-blind, randomized, placebo-controlled parallel pilot study was to investigate the acute effect of a single session of PEMFs stimulation by a PAP ion magnetic induction (PAPIMI) device on ANS activity, as measured by HRV, in patients with chronic musculoskeletal pain, and compare such effect with that induced by a sham (control) PAPIMI inductor. Thirty-two patients were randomized into two groups: PAPIMI intervention (PAP) (n = 17) and sham PAPIMI intervention (SHAM-PAP) (n = 15). HRV was assessed before and following the interventions. The PAP group showed a significant increase in all values of the time-domain parameters (SDNN, RMSSD, NN50, and pNN50) and the HF component of HRV, suggesting a parasympathetic effect. In contrast, the SHAM-PAP group showed no significant differences in all HRV indices following the intervention. Preliminary findings suggested that PAPIMI inductor could influence ANS activity and provided initial evidence of the potential physiological response induced by the PAPIMI device.