The use of instrument-assisted soft tissue mobilization (IASTM) has been documented to be effective for improving pain and function, but it is unclear whether it helps improve muscle performance in musculoskeletal diseases. This study investigated the effects of IASTM combined with exercise therapy on muscle endurance and pain intensity in patients with chronic neck pain. Forty-eight individuals with chronic neck pain were randomly divided into exercise therapy (ET, n = 24) and combined therapy (CT, n = 24) groups. For 4 weeks, each group underwent exercise therapy 3 days a week for a total of 12 sessions. The ET group received exercise therapy only. The CT group received IASTM combined with exercise therapy twice per week for a total of 8 sessions. The muscle endurance of the participants was assessed with the Deep Neck Flexor Muscle Endurance (DNFE) test and pain intensity with Visual Analogue Scale (VAS) at baseline and post-treatment. While both groups showed significant improvement in pain intensity (p < 0.05), the CT group showed a greater effect size for pain (CT group: Cohen's d = 3.28; ET group: Cohen's d = 2.12). The CT group showed significant improvement for muscle endurance (p < 0.05), whereas the ET group did not (p > 0.05). In the current study, the IASTM intervention combined with ET improved pain and muscular endurance in participants with chronic neck pain compared to exercise therapy alone. As an alternative method, IASTM intervention before exercise seems to increase the short-term recovery effect in chronic neck pain conditions.