Chronic neck pain (CNP) is associated with pain-related neuromuscular adaptations; however, in contrast to other superficial neck muscles, the influences of pain on hyoid muscles remain to be investigated. This study investigated how hyoid and superficial neck muscle activity differ between individuals with and without CNP during dynamic neck flexion and extension. In this observational cross-sectional, case–control study, 20 individuals with CNP and 20 sex- and age-matched asymptomatic controls were recruited. All participants performed dynamic neck flexion and extension in a crook-lying position at a controlled tempo. Surface electromyography was used to examine bilateral sternocleidomastoid (SCM), anterior scalene, upper trapezius, suprahyoid, and infrahyoid muscle activity. Normalised EMG values and their absolute phase-to-phase changes were analysed using linear mixed-effects models. A significant group × muscle interaction was observed (F = 3.34, p < 0.001, η² = 0.04), with higher normalised EMG values in the bilateral anterior scalene (left: GMR = 1.42, p = 0.01; right: GMR = 1.37, p = 0.03) and suprahyoid muscles (left: GMR = 1.42, p = 0.01; right: GMR = 1.37, p = 0.03) in individuals with CNP. In contrast, the phase-to-phase changes did not differ between the groups. These findings suggest that individuals with CNP exhibit selective alterations in muscle activation patterns.