This study aimed at investigating whether patients with neck-shoulder complaints from different aetiologies (work-related musculo-skeletal disorders, WMSD; whiplash associated disorders, WAD) show comparable muscle activation patterns, characterised by higher activation and lower relaxation levels of the trapezius muscles compared to healthy controls. Twenty healthy controls, 21 WMSD and 20 WAD patients with non-acute neck-shoulder pain were recruited for this cross-sectional study. Surface electromyography (sEMG) recordings were performed at the upper trapezius muscles during reference contractions, standardised computer tasks (typing and unilateral stress task), and rest measurements. sEMG was continuously recorded during these measurements. Outcome measures were root mean square (RMS) to study muscle activity, and relative rest time (RRT) to study muscle relaxation. Statistical analysis comprised the bootstrap technique and Kruskall-Wallis tests. Results showed no clear evidence for abnormal muscle activation patterns in WMSD and WAD patients compared to healthy controls. However, a tendency was observed for higher RMS levels during the reference contractions and computer tasks in both patient groups compared to healthy controls, and lower RRT levels at the non-dominant side during stress. Both patient groups also showed larger variability in RMS and RRT values. This variability has more often been reported in literature and may suggest the existence of subgroups of pain patients with corresponding different muscle activation patterns not related to aetiology. Future research may focus on identifying these subgroups of patients with neck-shoulder pain.