Background and Objectives This study constitutes the first attempt to describe the overlapping deprivations faced by Lebanese children (Lebanese) and that of the three sub-populations of refugees living in Lebanon: Palestinian refugees living in Lebanon, Palestinian refugees from Syria and Syrian refugees. Methods Using data from the United Nations International Children's Emergency Fund (UNICEF) Household Survey 2016 ( n = 10,555 Lebanese; 7,106 Palestinian refugees living in Lebanon; 2,768 Palestinian refugees from Syria and 5,891 Syrian refugee children aged 2 to 17 years old), we report on single and overlapping deprivations (at least two concurrent deprivations) using indicators related to survival (nutrition, health, water, sanitation and overcrowding), development (education) and protection (labor, exposure to violence and early marriage). Maternal education and geographical correlates of deprivation were explored using multivariable logistic regression models clustering for children in the same households. Main Results In terms of co-occurrence of deprivations, Syrian refugees had the highest prevalence in all age groups (68.5%, 2-4y and 65.7%, 6-17y), followed by Palestinian refugees from Syria (46.2%, 2-4y and 45.5%, 6-17y), Palestinian refugees living in Lebanon (28.9%, 2-4y and 23.7%, 6-17y), with Lebanese children having the lowest prevalence (13.2%, 2-4y and 15.3, 6-17y). About half of Palestinian refugees from Syria and Syrian refugees (6-17y) were deprived in protection and housing. Education deprivation is of primary concern for Syrian children. Higher maternal education was consistently associated with lower odds of co-occurrence of deprivations among children aged 6-17y. Conclusion This study highlights the importance of including refugee populations in reporting frameworks. This analysis additionally generates geographical and socio-economic profiles of the deprived children and identifies key deprivation areas of the affected sub-groups to inform effective policy design especially in light of the prevailing economic crisis.