Background: Chronic musculoskeletal pain (CMP) is a multidimensional condition involving both peripheral and central mechanisms, with increasing evidence supporting an interplay between subjective pain perception and autonomic nervous system (ANS) function. However, few studies have explored whether a single non-invasive intervention can concurrently modulate both domains. Objectives: To evaluate the short-term effects of a single session of Pulsed Electromagnetic Field (PEMF) therapy—administered via the PAP Ion Magnetic Induction (PAPIMI™) device—on subjective pain intensity and heart rate variability (HRV) parameters in individuals with CMP. The relationship between perceived pain relief and physiological autonomic adaptations was also explored. Methods: Thirty adults with CMP underwent a single PAPIMI™ session. Subjective pain intensity was measured using the Numeric Pain Rating Scale (NPRS), while autonomic function was assessed via HRV. Pre- to post-intervention changes were analyzed using the Wilcoxon Signed-Rank test, while Spearman’s correlation was computed to assess associations between post-intervention changes in subjective perceived pain and HRV parameters. Results: A significant reduction in NPRS scores (p < 0.001) was found after PAPIMI intervention. Also, a significant increase in specific parasympathetic-related HRV indices, namely, RMSSD (p = 0.015) and HF power (p = 0.029), was observed. No significant correlations were found between post-intervention changes in pain perception and HRV metrics. Conclusions: A single PAPIMI session induced both analgesic effects and improvements in autonomic balance in individuals with CMP. These findings underscore the potential of PAPIMI as a non-pharmacological approach for rapid pain modulation and systemic rebalancing.