Abstract Background Persistent or recurrent neck pain is associated with perturbations in the autonomic nervous system balance, and nociceptive stimulation has been seen to influence this balance. However, very few prospective studies have addressed the extent to which changes in pain associate with changes in autonomic cardiac regulation. Therefore, we investigated if changes in pain vary with changes in heart rate variability in a cohort of patients treated for persistent or recurrent neck pain. Method This analysis is based on data from a randomized controlled trial in which participants were given home stretching exercises with or without spinal manipulative therapy for two weeks. As the effectiveness of the intervention (home stretching exercises and spinal manipulative therapy) was found to be equal to the control (home stretching exercises alone), all 127 participants were studied as one cohort in this analysis. During the intervention, pain levels were recorded using daily text messages, and heart rate variability was measured in the clinics three times over two weeks. Two approaches were used to classify patients based on changes in pain intensity: 1) Clinically important changes in pain were categorized as either "improved" or "not improved" and, 2) Pain development was measured using pain trajectories, constructed in a data driven approach. The association of pain categories and trajectories with changes in heart rate variability indices over time were then analysed using linear mixed models. Results Heart rate variability did not differ significantly between improved and not-improved patients, nor were there any associations with the different pain trajectories. Conclusions In conclusion, changes in pain after home stretching exercises with or without spinal manipulative therapy over two weeks were not significantly associated with changes in heart rate variability for patients with persistent or recurrent neck pain. Future studies should rely on more frequent measurements of HRV during longer treatment periods. Trial registration The trial was registered at ClinicalTrials.gov, registration number: NCT03576846.