Background In Bangladesh, as in other low- and middle-income countries, parents frequently migrate to other areas, often for employment opportunities, leaving their children behind with the hope that their earnings will contribute to securing a better future for them. However, the absence of parents due to migration can have negative implications for the well-being of these left-behind children. Despite the existence of studies investigating this phenomenon, the evidence thus far has produced inconclusive findings, with no specific data available from Bangladesh. Therefore, the objective of this study was to examine the effects of parental migration on the early childhood development of left-behind children in Bangladesh. Methods The present study utilized data from the Bangladesh Multiple Indicator Cluster Survey (MICS) conducted in 2019. A sample of 8,833 children aged 3–4 years was included in the analysis. The Early Childhood Development Index (ECDI) and its individual domains served as the outcome variables of interest. The primary explanatory variables considered in the analysis were father migration, mother migration, migration of both parents, and migration of either parent. To assess the association between the outcomes and explanatory variables, multilevel logistic regression analysis was employed, controlling for relevant covariates. Results Approximately 29% of all children in the study were not developmentally on track, as measured by the ECDI. When examining the individual domains of the ECDI, only 9% of the total children demonstrated developmental progress in the learning domain. Regarding the association between parental migration and ECDI outcomes, we observed a 26% decrease in the likelihood of overall ECDI among children with a migrated father (OR: 0.74, 95% CI: 0.54–0.93). This decrease became even more pronounced, reaching 37% (OR: 0.63, 95% CI: 0.48–0.97), among children with both parents migrated, compared to children with neither parent migrated. Conclusion The findings of this study indicate that parental migration, especially when both parents are involved, has a substantial negative impact on the likelihood of achieving favourable ECDI outcomes for children in Bangladesh. To ensure the optimal development of children with migrating parents, it is crucial to strengthen early childhood development education programs and implement robust social safety nets. These efforts should specifically target the unique needs and challenges faced by children with migrated parents, providing them with the necessary support and resources for their holistic development.