The aim of this study was to investigate associations of workplace bullying and harassment with headache, stiffness of the neck or shoulders, lumbago, and pain of two or more joints. The subjects in this cross-sectional study were recruited from workers (n = 1,913) at 35 healthcare or welfare facilities in Japan. Because of non-participation or missing data, the number of subjects included in the analysis varied (response rate ≥ 77.1%). Workplace bullying and harassment were assessed using the Negative Acts Questionnaire. Depression was assessed using the Brief Job Stress Questionnaire. The frequency of pain experienced by workers in the previous month was evaluated using a four-point scale. Many of the associations of person-related bullying, work-related bullying, and sexual harassment with headache, stiffness of the neck or shoulders, lumbago, and pain of two or more joints were positive and significant (p < 0.05). Even after adjustment for depression, some of the associations remained significant (p < 0.05). For example, changes in the prevalence ratio for headache associated with a 1-point increase in the work-related bullying score were 1.05 (95% confidence interval (CI) 1.01 to 1.09) in men and 1.03 (95% CI 1.01 to 1.05) in women after adjustment for age, marital status, employment status, work shift, and depression.