Abstract Background The prevalence of effort-reward imbalance (ERI) among qualified childcare workers in Germany is currently estimated at around 65%. High rates of burnout and musculoskeletal symptoms (MS) have also been reported for this group. Previous longitudinal studies show inconsistent results with regard to the association between ERI and MS. As yet, no longitudinal studies have been conducted to investigate the association between ERI and burnout or MS in childcare workers. This study aims to investigate the extent to which a relationship between ERI and MS or burnout can be observed in childcare workers in Germany on a longitudinal basis. Methods In 2014 childcare workers (N = 199, response rate: 57%) of a provider of facilities for children and youth in Hamburg were asked about stress and health effects in the workplace. Follow-up was completed one year later (N = 106, follow-up rate: 53%) For the baseline assessment, ERI was determined as the primary influencing factor. Data on MS was recorded using the Nordic questionnaire, and burnout using the personal burnout scale of the Copenhagen Burnout Inventory (CBI). The statistical analysis was carried out using multivariate linear and logistic regression. Results At baseline ERI was present in 65% of the sample population. The mean burnout score at the time of follow-up was 53.7 (SD: 20.7); the prevalence of MS was between 19% and 62%. ERI was identified as a statistically significant factor for MS, after adjusting especially for physical stress (lower back: OR 4.2; 95% CI: 1.14 to 15.50, neck: OR 4.3; 95% CI: 1.25 to 15.0, total MS: OR 4.0; 95% CI: 1.20 to 13.49). With regard to burnout, a relative increase of 10% in the ERI ratio score increased the burnout score by 1.1 points (p = 0.034). Conclusions ERI was revealed to be a major factor in relation to MS and burnout in childcare workers. Based on this observation worksite interventions on the individual and organizational level should be introduced in order to prevent ERI.