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Background: This two-arm, parallel, pragmatic, multicenter, clinical randomized, controlled trial with a 12-week follow-up period aimed to compare the effectiveness of pharmacopuncture therapy and physical therapy strategies for chronic neck pain. Methods: Eight sessions of pharmacopuncture therapy or physical therapy were administered within 2 weeks. The primary outcome was the visual analogue scale (VAS) score for neck pain. The secondary outcomes were the scores of the Northwick Park questionnaire (NPQ), VAS score for radiating arm pain, numeric rating scale (NRS) for neck and arm bothersomeness, neck disability index (NDI), patient global impression of change (PGIC), 12-item short form health survey (SF-12), and EuroQoL 5-dimension 5-level (EQ-5D-5L) instrument. The protocol was registered with Clinicaltrials.gov (NCT04035018) and CRIS (KCT0004243). Results: We randomly allocated 101 participants with chronic neck pain to the pharmacopuncture therapy (n = 50) or physical therapy group (n = 51). At the primary endpoint (week 5) the pharmacopuncture therapy group showed significantly superior effects regarding VAS score for neck pain and arm bothersomeness, NRS for neck pain, NDI, NPQ, and PGIC compared with the physical therapy group. These effects were sustained up to 12 weeks after follow-up. Conclusion: Compared with physical therapy, pharmacopuncture therapy had superior effects on the pain and functional recovery of patients with chronic neck pain. [ABSTRACT FROM AUTHOR]