Objective: Prolonged periods of living in prefabricated houses (PHs) may increase the risk of musculoskeletal (MSK) symptoms; however, the association is not clear. This study aimed to investigate the association between continued residence in PHs and MSK pain in a population affected by a natural disaster, the Great East Japan Earthquake (GEJE) survivors. Design, setting, and participants: A panel study was conducted including 1,059 and 792 survivors at 2 and 4 years, respectively, after the GEJE, using a self-reported questionnaire. Those with no response on living status and those who did not live in a PH were excluded. Participants were classified into two groups by living status: continued residence in a PH (lived in a PH during both periods) or moving out of a PH (lived in a PH in the first period and did not live in a PH in the second). Primary outcome measure: MSK pain included lower back, shoulder, knee, hand or foot, and neck pain. Changes in the occurrence of MSK pain during the two periods were assessed and defined as “new-onset” and “continuing” MSK pain. Multiple logistic regression analysis was used to examine the influence of continued residence in a PH on new–onset and continuing MSK pain. Results: Continued residence in a PH was significantly associated with new–onset MSK pain, even after adjustment for covariates (adjusted odds ratio [OR]: 2.18, 95% confidence interval [95% CI]: 1.25–3.79, p = 0.006). Participants who continued living in a PH had higher rates of continuing MSK pain than those who moved out; however, the difference was not significant (adjusted OR: 1.69, 95% CI: 0.94–3.05, p = 0.079). Conclusion: Continued residence in a PH was associated with new-onset MSK pain among survivors. Public support should be provided to such people to ensure a more comfortable life.