Exercise therapy is the most common approach for people with chronic neck pain (CNP). Although well‐established, it remains unknown which type of exercise is the best for treating this condition. Moreover, pain processing can play a role in the persistence of pain and in the response to interventions. Thus, the aim of this randomized controlled trial is to compare the acute and long‐term effects of two exercise protocols (specific and non‐specific) on pain and pain processing in individuals with CNP. One hundred and ten participants aged between 18 and 65 years who have had non‐specific neck pain for more than 3 months will be recruited. They will be randomized and allocated into two groups (specific exercises and non‐specific exercises) and both groups will perform an exercise programme twice a week for 8 weeks. Both programmes are divided into two progressive and individualized phases. The primary outcomes are change in pain intensity after 8 weeks of exercise and exercise‐induced hypoalgesia, and secondary outcomes are pressure pain threshold, temporal summation of pain, conditioned pain modulation, the Neck Disability Index, the Baecke Physical Activity Questionnaire, and the Global Perception of Change Scale. Outcomes will be assessed at baseline, after 8 weeks of intervention, and at 6‐month follow‐up.