Sleep disturbance is a common symptom after natural disasters. Although musculoskeletal pain also increases after natural disasters, its relation to sleep disturbance is not clear. The purpose of this study was to determine the influence of musculoskeletal pain on new-onset sleep disturbance among survivors after the Great East Japan Earthquake (GEJE). A prospective cohort study was conducted with the survivors of the GEJE at two and three years after the earthquake. New-onset sleep disturbance was defined as sleep disturbance absent at two years and present at three years after the earthquake. The sites of musculoskeletal pain included low back, shoulder, knee, and hand or foot. The number of musculoskeletal pain sites at two years after the earthquake was divided into three categories (0, 1, and 2 or more). Univariate and multivariate logistic regression models were used to calculate the odds ratio (OR) and 95% confidence interval (95%CI) for new-onset sleep disturbance according to the number of musculoskeletal pain sites. A total of 1,102 survivors were included in this study and 14.6% of the participants reported new-onset sleep disturbance. Using "0" as a reference, the adjusted ORs (95% CI) for new-onset sleep disturbance were 2.43 (1.55-3.80) in "1" and 2.96 (1.88-4.64) in "2 or more", respectively (P for trends < 0.001). In conclusion, this is the first study showing higher incidence of sleep disturbance among survivors with musculoskeletal pain after the GEJE. Care for musculoskeletal pain is important to prevent sleep disturbance after natural disasters.