Background: In the current era, malnutrition among children considers main reason of morbidity and mortality in the world scenario while more specifically in developing countries. Malnutrition in children severely affects their physical growth and academic achievements. This study aimed to find out the effect of socioeconomic factors on malnutrition, children aged under 5 years in Multan district of Punjab province, Pakistan. The study used the data of 2497 children, obtained from Multiple Integrated Cluster Survey 2018 and employed Binary logistic regression approach for empirical estimation the effects of socioeconomic factors on malnutrition among children. Results: Empirical estimates of the study specified the prevalence of higher frequency of stunting (18.58), wasting (28.43) and underweight (19.54) among children particularly in rural areas of the study district Multan. Stunting status was significantly associated with children of some month (OR = 1.247, CI 95% 0.543–1.546), family size (OR = 0.589, CI 95% 0.431–3.715), maternal education (OR = 1.432, CI 95% 0.528–1.972), wealth quintile (OR = 2.174, CI 95% 1.234–3.376) and sanitation facility (OR = 0.789, CI 95% 0.627–1.987). Wasting status was mostly correlated with male children (OR = 1.208, CI 95% 0.769–1.352), children of urban areas (OR = 0.594, CI 95% 0.476–1.987) and food shortage (OR = 1.367, CI 95% 0.782–2.543). Underweight status was close relationship with male gender (OR = 1.213, CI 95% 0.821–2.897), incomplete immunization (OR = 1.342, CI 95% 1.041–2.658) and treated water access (OR = 0.689, CI 95% 0.542–2.743). Conclusion: In this study, prevalence of higher-level malnutrition was estimated due to lower socioeconomic status among major population in the community specifically in rural areas. The government needs to enhance economic opportunities, promote healthcare education, increase nutritional access and generate improving personal hygiene habits through appropriate economic, political and social policy measures. The outcome of these policies will enhance individual economic resources; ensure nutritional safety, increasing maternal schooling and helpful for improving child health.