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Objectives Chronic shoulder pain is one of the common musculoskeletal problems involved with unreleased pain and functional dysfunction, and it can even evolve into central sensitisation. Some manual therapy aggravated pain and central sensitisation. Joint position sense therapy (JPST) is moderate joint proprioception training compared with vigorous exercises or aggressive hands-on therapy. This study will explore the expression of central sensitisation in chronic shoulder pain and the effect of JPST on shoulder functional dysfunction and pain. Methods Pressure pain threshold (PPT) was assessed together with four sites at the deltoid, upper trapezius, brachioradialis and tibialis anterior muscles among 30 chronic shoulder pain and 30 non-chronic pain patients. A total of 30 patients with chronic shoulder pain were randomly divided into the JPST group and a control group. The JPST group underwent additional shoulder joint position sense training. The efficiency outcomes were the Disabilities of the Arm, Shoulder, and Hand Questionnaire (DASH), Visual Analog Scale (VAS) and PPT evaluated at baseline and after the intervention. Results Significant differences were observed in PPT values at brachioradialis (P < 0.05), deltoid (P < 0.01) and trapezius (P < 0.001) among non-chronic and chronic groups, but not in tibialis anterior muscle (P > 0.05). Although both control and JPST intervention were effective in improving DASH, pain intensity and PPT values in the upper limb, outcomes in the JPST group showed significant differences from the control group. Conclusions A generalised hyperalgesia changes limited to the upper limb were noticed in chronic shoulder pain. Joint position sense therapy had a beneficial effect on pain control and functional dysfunction in chronic shoulder pain patients.