BackgroundWork-related musculoskeletal disorders (WMSDs) have become increasingly common among health-related professionals. Special education personnel who serve students with disabilities often experience physical strains; however, WMSDs have been overlooked in this population. The objectives of this study were to investigate the work-related ergonomics-associated factors in this population and to evaluate their correlation with the WMSDs prevalence.MethodsA questionnaire with three domains, namely demographics, prevalence of work-related musculoskeletal disorders, and ergonomic factors, designed by our research team was delivered to educators who work in special education schools.ResultsApproximately 86 % of the 388 special education school teachers and teacher’s aides in this study experienced musculoskeletal disorders. The lower back, shoulder, and wrist were the three most affected regions. A logistic regression analysis revealed that the participants’ background factors, namely >5.5 years of experience (odds ratio [OR] = 4.090, 95 % CI: 1.350-12.390), students with multiple disorders (OR = 2.412, 95 % CI: 1.100-5.287), and other work-related ergonomic factors (assistance in diaper changing and others duties), were strongly associated with the prevalence of WMSD. Nap habit (OR = 0.442, 95 % CI: 0.230-0.851) and having teaching partners in the same class (OR = 0.486, 95 % CI: 0.250-0.945) resulted in low possibility of acquiring WMSDs. The use of supportive devices was associated with a low WMSD prevalence.ConclusionsThe present study revealed an association between WMSDs and specific job features among teachers and teacher’s aides in special education schools. Future efforts should emphasize examining safe student-handling ergonomics, formulating policies regarding student-teacher ratio, incorporating mandatory break times at the workplaces, and promoting personal health for preventing work-related injuries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12889-016-2777-7) contains supplementary material, which is available to authorized users.