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The objective of the current study is to identify the risk factors for malnutrition among the age of under-five children’s in Pakistan. This is secondary data analysis for the data taken from Pakistan Demographic and Health Survey (PDHS 2017–18) and was analyzed by implementing quantile regression analysis. The sample size included 12,708 alive children in the study, for which the data collection period was from November 22, 2017, to April 30, 2018. The prevalence of malnutrition among boys is high (51.2%). Older age mother’s children have more prevalence of malnutrition (20.7%). A child born with small body size (underweight: Q_0.25: − 0.625; Q_0.50: − 0.623; Q_0.75: − 0.426 and wasting: Q_0.50: − 0.513); having uneducated mother (underweight: Q_0.25: − 0.387; Q_0.50: − 0.247; Q_0.75: − 0.328), belonged to a poor household (underweight: Q_0.50: − 0.251),residing in rural areas (underweight: Q_0.25: − 0.443 …