Objective To explore the effects of contralateral manual acupuncture (MA) on patients with chronic shoulder pain. Methods Eighty patients with chronic shoulder pain were randomly allocated to receive contralateral MA (n=38) for 4 weeks or to remain on a waiting list while receiving conventional orthopaedic therapy (n=42). Visual analogue scale (VAS) scores were taken as the primary outcome measure and used for a priori power calculation. Secondary outcome measures for the assessment of shoulder mobility and quality of life included the Jobe test, the Constant-Murley (CM) score, the Disabilities of the Arm, Shoulder and Hand (DASH) score, and the 36 item Short Form Health Survey (SF-36). Results Intention-to-treat (ITT) analysis demonstrated significant pain relief with contralateral acupuncture, with mean differences in VAS scores compared to the waiting list group of −19.4 (−28.0 to −10.8) at 2 weeks, −40.4 (−49.0 to −31.8) at 4 weeks, −41.1 (−49.7 to −32.5) at 8 weeks, and −40.9 (−49.5 to −32.3) at 16 weeks. CM and DASH scores were also improved at all time points (p<0.01). Shoulder mobility, physical functioning, social functioning and mental health components of the SF-36 were also improved by contralateral acupuncture at 8 weeks. No significant adverse effects were observed. Conclusions These results demonstrate beneficial effects of contralateral acupuncture in the treatment of chronic shoulder pain, both in terms of pain and function. Future research is required to compare directly the effects of local and contralateral acupuncture and to quantify the specific and non-specific effects. Trial Registration Number NCT01733914.