A cross-sectional questionnaire study was carried out on nursery school (NS) teachers in public nursery schools in N city in Japan to determine the magnitude of associations of probable risk factors with neck, shoulder, and arm pain, adjusting for potential confounders in logistic regression models. Of 1438 subjects, responded to the questionnaire, 959 NS teachers in charge of a separate or mixed group of children were subjected to analyses. Prevalence of neck and/or shoulder pain was 33.6%-35.4% in NS teachers in charge of children aged 0, 0-1, 4, and 5 in contrast to 25.0-29.8% in those in charge of children aged 1, 2, and 3. The prevalence of neck/shoulder pain tended to increase with the length of employment in all groups classified according to the age of children under care. In a logistic regression model that simultaneously adjusted demographic and personal variables, length of employment and care for children aged 0 in the workplace were found significantly associated with musculoskeletal pain. In further logistic models, pain in the neck/shoulders and arms had associations with some specific variables: care for children aged 0, holding/lifting a child/material, overwork, and poorly supported job situations. The odds ratios for those variables varied from 1.37 to 2.41. This results suggest that pain in the neck/shoulders and arms is induced by a wide variety of risk factors in NS teachers that include high physical workload, long working hours, job demand-support imbalance, and cumulative influence of workloads.