Neck pain is a widespread medical condition among office workers worldwide. This study aimed to compare physical exercises, including basic body awareness, neck-specific training exercises and ergonomic modifications, and ergonomic modifications alone in the management of chronic non-specific neck pain (NSNP) among office workers. Sixty participants were randomly allocated to an experimental group (physical exercises and ergonomic modifications) or a control group (ergonomic modifications) and received the intervention two times a week for eight weeks. The Numerical Pain Rating Scale, Neck Disability Index, Health and Safety Stress Tool, and Short Form Health Survey-36 were used to measure pain, disability, job stress, and quality of life at baseline, and at weeks 4 and 8 of the study period. A repeated measure ANOVA was used to determine the within-group significant differences and an independent t-test was utilized to compare group differences. The baseline data of the experimental and control groups showed no significant difference (p ≥ 0.05). The 2 × 3 mixed models ANOVA showed a significant difference in pain intensity (p = 0.001, ηp² = 0.042), functional disability (p = 0.001, ηp² = 0.052), work-related stress (p = 0.001, ηp² = 0.036), and QoL (p = 0.012, ηp² = 0.025). Four weeks post-intervention, the experimental group showed significant changes in primary (pain intensity and disability) (1.9; 95% confidence interval 1.65–2.14) and secondary (quality of life and work-related stress) outcomes (p < 0.001). The same gradual improvement in these variables was observed in the 8-week follow-up (p < 0.001). There was a significant improvement in clinical outcomes following the application of physical exercises with ergonomic modifications for chronic NSNP among office workers. This is significant for office workers because it suggests the importance of incorporating physical exercises into their daily routine and making ergonomic changes to their workspaces.