Evidence reports positive effects of neck motor control and aerobic exercises (AEs) to improve pain in individuals with temporomandibular disorders (TMD) and neck pain. A single bout of exercise typically leads to an increase in pain thresholds up to 30 min post-exercise, known as exercise-induced hypoalgesia (EIH). Studies evaluating the effects of aerobic and neck motor control exercises on EIH in individuals with chronic neck pain and TMD are limited. Measuring treatment effects and determining the clinical significance based on exercise types and loads and EIH response can improve clinical outcomes and adherence to exercise programmes. This study was designed to determine the clinical significance of EIH after neck motor control and aerobic training in participants with TMD and neck pain. Participants between 18 and 60 years with neck pain and/or TMD will be randomized to neck motor control or aerobic training groups. Participants will be assessed before, immediately after and 15 min after three treatment sessions within a 12-week exercise programme. Assessments will include pain intensity, pressure pain thresholds and tolerance of masticatory and neck muscles, and the Global Rating of Change Scale. EIH response will be calculated in absolute and relative changes by subtracting the post- from the pre-exercise values. Distribution-based (e.g., effect size) and anchor-based (e.g., receiver operating characteristics) methods will be performed to determine the clinical significance of EIH (minimal important difference).