BackgroundAltered thickness, cross-sectional area and activity of deep neck muscles have frequently been reported in patients with chronic non-specific neck pain (CNNP). It is claimed that these muscles do not recover spontaneously. These muscles provide a considerable amount of cervical stability. Therefore, various therapeutic exercises have been recommended to recover from resulting complications. However, most exercise protocols do not target deep neck muscles directly. Thus, this might be a reason for long-lasting complications. Accordingly, the purpose of the present study is to discuss a randomized controlled trial (RCT) protocol in which we aim to investigate and compare the effects of neck-specific exercise programmes versus general exercise programmes in patients with CNNP.MethodsA 2*2 factorial RCT with before-after design. Sixty-four participants with CNNP will be recruited into the study. They will be randomly divided into two groups, including specific neck exercise and general exercise. Each exercise programme will be carried out three times a week and will last for 8 weeks. Primarily, dorsal and ventral neck muscle thickness, pain and disability and secondarily, muscle strength, quality of life, sleep quality, fear avoidance and neck range of motion will be assessed at the baseline and immediately at the end of the exercise protocol.DiscussionThe results of this study will inform clinicians on which type of exercise is more beneficial for patients with CNNP.