Background: Prevalence of musculoskeletal pain is high in jobs with high physical work demands. An aerobic exercise intervention targeting cardiovascular health was evaluated for its long term side effects on musculoskeletal pain. Objective: The objective was to investigate if aerobic exercise affects level of musculoskeletal pain from baseline to 4- and 12-months follow-up. Methods: One-hundred-and-sixteen cleaners aged 18–65 years were cluster-randomized. The aerobic exercise group (n = 57) received worksite aerobic exercise (30 min twice a week) and the reference group (n = 59) lectures in health promotion. Strata were formed according to closest manager (total 11 strata); clusters were set within strata (total 40 clusters, 20 in each group). Musculoskeletal pain data from eight body regions was collected at baseline and after 4- and 12-months follow-up. The participants stated highest pain in the last month on a scale from 0, stating no pain, up to 10, stating worst possible pain. A repeated-measure 2 × 2 multi-adjusted mixed-models design was applied to compare the between-groups differences in an intention to treat analysis. Participants were entered as a random effect nested in clusters to account for the cluster-based randomization. Results: Clinically significant reductions (>30%, f 2 > 0.25) in the aerobic exercise group, compared to the reference group, in pain intensity in neck, shoulders, arms/wrists were found at 12-months follow-up, and a tendency (p = 0.07, f 2 = 0.18) to an increase for the knees. At 4-months follow-up the only significant between-group change was an increase in hip pain. Conclusions: This study indicates that aerobic exercise reduces musculoskeletal pain in the upper extremities, but as an unintended side effect may increase pain in the lower extremities. Aerobic exercise interventions among workers standing or walking in the majority of the working hours should tailor exercise to only maintain the positive effect on musculoskeletal pain.