BACKGROUND: Micro-randomized trials (MRTs) enhance the effects of mHealth by determining the optimal components, timings, and frequency of interventions. Appropriate handling of missing values is crucial in clinical research; however, it remains insufficiently explored in the context of MRTs. Our study aimed to investigate appropriate methods for missing data in simple MRTs with uniform intervention randomization and no time-dependent covariates. We focused on outcome missing data depending on the participants' background factors. METHODS: We evaluated the performance of the available data analysis (AD) and the multiple imputation in generalized estimating equations (GEE) and random effects model (RE) through simulations. The scenarios were examined based on the presence of unmeasured background factors and the presence of interaction effects. We conducted the regression and propensity score methods as multiple imputation. These missing data handling methods were also applied to actual MRT data. RESULTS: Without the interaction effect, AD was biased for GEE, but there was almost no bias for RE. With the interaction effect, estimates were biased for both. For multiple imputation, regression methods estimated without bias when the imputation models were correct, but bias occurred when the models were incorrect. However, this bias was reduced by including the random effects in the imputation model. In the propensity score method, bias occurred even when the missing probability model was correct. CONCLUSIONS: Without the interaction effect, AD of RE was preferable. When employing GEE or anticipating interactions, we recommend the multiple imputation, especially with regression methods, including individual-level random effects.