IntroductionSeveral studies have shown that residents of urban informal settlements/slums are usually excluded and marginalised from formal social systems and structures of power leading to disproportionally worse health outcomes compared to other urban dwellers. To promote health equity for slum dwellers, requires an understanding of how their lived realities shape inequities especially for young children 0–4 years old (ie, under-fives) who tend to have a higher mortality compared with non-slum children. In these proposed studies, we aim to examine how key Social Determinants of Health (SDoH) factors at child and household levels combine to affect under-five health conditions, who live in slums in Bangladesh and Kenya through an intersectionality lens.Methods and analysisThe protocol describes how we will analyse data from the Nairobi Cross-sectional Slum Survey (NCSS 2012) for Kenya and the Urban Health Survey (UHS 2013) for Bangladesh to explore how SDoH influence under-five health outcomes in slums within an intersectionality framework. The NCSS 2012 and UHS 2013 samples will consist of 2199 and 3173 under-fives, respectively. We will apply Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy approach. Some of SDoH characteristics to be considered will include those of children, head of household, mothers and social structure characteristics of household. The primary outcomes will be whether a child had diarrhoea, cough, fever and acute respiratory infection (ARI) 2 weeks preceding surveys.Ethics and disseminationThe results will be disseminated in international peer-reviewed journals and presented in events organised by the Accountability and Responsiveness in Informal Settlements for Equity consortium and international conferences. Ethical approval was not required for these studies. Access to the NCSS 2012 has been given by Africa Population and Health Center and UHS 2013 is freely available.