Chronic neck pain is a common human health problem. Changes in scapular posture and alteration of muscle activation patterns of scapulothoracic muscles are cited as potential risk factors for neck pain. The purpose of this study was to compare the effects of neck exercise training (NET) with and without scapular stabilization training (SST) on pain intensity, the scapula downward rotation index (SDRI), forward head angle (FHA) and neck range of motion (ROM) in patients with chronic neck pain and scapular dyskinesia. A total of sixty-six subjects with chronic neck pain and scapular dyskinesia were randomly divided into three groups: neck exercise training, n = 24, combined training (NET + SST), n = 24 and a control group, n = 24. Pain intensity, SDRI, FHA and ROM were measured by the numerical rating scale, caliper, photogrammetry and IMU sensor, respectively. When the combined intervention group consisting of NET and SST was compared with NET alone at six weeks, there was a statistically significant difference in pain intensity, SDRI, FHA and cervical ROM for flexion and extension (p ≤ 0.05). Adding scapular exercises to neck exercises had a more significant effect in decreasing pain intensity, SDRI, FHA and increased cervical ROM than neck exercises alone in patients with chronic neck pain. These findings indicate that focus on the scapular posture in the rehabilitation of chronic neck pain effectively improves the symptoms.