Background Previous studies have shown that morning types are less sensitive to pain. This study aimed to examine the relationship between chronotypes and musculoskeletal problems in workers with musculoskeletal burdens at work. Methods This cross-sectional study included 119 male production workers from a large automobile manufacturing plant. All the participants worked 2 shifts and worked on the automobile assembly line. Data were obtained using structured questionnaires, including the reduced Morningness-Eveningness Questionnaire (rMEQ), and musculoskeletal symptom questionnaire. Participants with an rMEQ score of 18 points or more were defined as morning-type workers (MTWs). Participants whose scores were less than 18 points were defined as neither-type workers (NTWs). Results The arithmetic mean age was 51.8 ± 5.3 years. MTWs and NTWs accounted for 35.3% and 64.7% of the total participants, respectively. Evening- and intermediate-type workers accounted form 6.7% and 58.0% of the participants, respectively. There was no significant difference in the health indicators when the MTW and NTW groups were compared. However, the musculoskeletal symptom questionnaire demonstrated a significant difference between the MTW and NTW groups. In the preceding year, the MTW group had significantly lower musculoskeletal pain and treatment ratios compared to the NTW group (35.7% vs. 62.3%, p = 0.005 and 14.3% vs. 32.5%, p = 0.031, respectively). After adjusting for variables, the odds ratio (OR) for musculoskeletal pain was significantly higher in the NTW group than in the MTW group (OR, 3.112; 95% confidence interval, 1.285-7.535; p = 0.012). Conclusions In this study, the musculoskeletal pain ratio was significantly lower for MTWs when compared to NTWs. Chronotypes could play an important role in work-related musculoskeletal disorders. Further, larger-scale, follow-up studies on chronotypes are required to assist in the prevention of musculoskeletal disorders in future.