Background and Objective: Maharashtra accounts for the highest number of Covid-19 cases in India. The pandemic and the subsequent lockdown have exacerbated the malnutrition crisis in the state. Many districts in the state are fighting a dual battle of COVID-19 and undernutrition. The numbers are really alarming given that the situation is going to aggravate further in the absence of social protection schemes. Even though children in the state have shown resilience against the SARS-CoV-2 than adults, pre-existing inequalities and undernutrition pose enormous risk. Drawing insights from the Alkire Foster measure, the study endorses a multidimensional approach to measure the complex and multifaceted nature of early childhood health. Methods: The study utilizes the fourth round of District Level Health Survey to provide district-level estimates of the inequalities in multidimensional health deprivations among children in Maharashtra. Multidimensional Health Poverty Index (MHPI), concentration curves, normalized concentration index, geographical maps, and logistic regression model are used to analyze the data at the multiple levels of state, districts, rural-urban residence and gender. The implications of the pandemic on the childhood undernutrition and the public health care system are also discussed. Results: The findings indicate that multidimensional health inequalities manifest primarily among the weaker sections of society. The MHPI of under-five children is 0.297 with 46.8 percent of them identified as multidimensionally health poor and experiencing an average of 63.4 % of weighted deprivations. The rural areas are home to a much larger number of multidimensional health poor than urban ones. The spatial profiling shows that worst performers are mostly clustered in and around Marathwada region which is one of the backward areas of Maharashtra. The main predictors of multidimensional health poverty among under-five children are low asset index, educational and employment status of the parents and health conditions of the mother. Conclusion: Recognizing the regional heterogeneity in the incidence of multidimensional health poverty and distribution calls for strengthening COVID-19 intervention strategies attuned for specific district targets.