Objectives To evaluate the prevalence of musculoskeletal disorders (MSD) and associated factors among office workers working in activity-based workplace (ABW). Methods 42 office workers with ABW and 68 office workers as control participated. Nordic Musculoskeletal Questionnaire, Baecke Physical Activity Questionnaire, Copenhagen Psychosocial Questionnaire III, and Fear Avoidance Beliefs Questionnaire were used and Pain pressure threshold (PPT) measured. Results There were no significant differences in the prevalence of MSDs in most body areas during the between ABW and control group. ABW group experienced significantly (p<0.05) more right wrist, hand, and finger pain in the past 6 months when compared with the control group. ABW group demonstrated significantly (p<0.05) more work-related physical activity and daily time spent standing. There were no significant differences in other pain-related factors measured. Conclusions Office workers with ABW had a similar prevalence of MSDs to office workers with a designated workplace and no differences in associated factors.