Altered 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.