The purpose of the study was to examine the effects of a workplace physical exercise intervention on the perceived intensity of headache and the intensity of symptoms in the neck and shoulders, as well as on the extension and flexion strength of the upper extremities. The study was a cluster randomized controlled trial. The cross-over design consisted of physical exercise intervention (15 weeks) and no-intervention (15 weeks). The subjects (n=53) were office workers (mean age 46.6 (SD 8.4)) who reported headache (n=41) symptoms in the neck (n=37) or shoulders (n=41), which had restricted their daily activities during the last 12 months. Pain symptoms were measured using the Borg CR10 scale and muscular strength with a 5RM test. Statistical analyses were based on linear mixed models. Physical exercise intervention resulted in a slight, but statistically significant, decrease in the intensity of headache and neck symptoms, as well as an increase in the extension strength of the upper extremities. The mean decrease in headache during the 5-week period was 0.64 CR10 (95% CI 0.28-1.00) (P=0.001) or 49% (95% CI 22-77), and 0.42 CR10 (95% CI 0.11-0.72) (P=0.002) or 49% (95% CI 13-85) in the intensity of neck symptoms. The mean increase in the extension strength of the upper extremities was 1.3 kg (95% CI 0.5-2.1) (P=0.001) or 4% (95% CI 1-6). The intervention had no effect on the intensity of shoulder symptoms or the flexion strength of the upper extremities. Specific exercise may be clinically important to alleviate headache and neck symptoms.