Malnutrition among children is an important public health problem in Pakistan. Conventional indicators (stunting, wasting and underweight) are well known. However, there is a need for aggregate indicators in this perspective. The goal of this study is to assess the prevalence and trends of malnutrition among Pakistani children under the age of five using the so-called composite index of anthropometric failure (CIAF), a tool for calculating the whole aggregate burden of malnutrition. The data were extracted from the Pakistan Demographic and Health Survey 2012–2013. Mothers’ education and socioeconomic statuses (SES) were assessed as important factors in malnutrition. Chi-squared analysis was used to check the bivariate association, and multiple logistic regression was used to identify the significant correlates of child malnutrition. Moreover, multiple correspondence analysis (MCA) was applied to strengthen the use of CIAF as an outcome variable. The study looked at 3071 children under the age of five, with 52.2% of them falling into the CIAF. Children of educated mothers had 43% fewer odds of being malnourished (OR (Odd Ratio) = 0.57, 95% CI (Confidence Interval) = 0.44–0.73). Additionally, a decreasing trend in malnutrition was found with increasing SES. There is a need to improve maternal education. Such programs focusing on increasing women’s autonomy in making home decisions should be established. Furthermore, long-term interventions for improving home SES and effective nutritional methods should be examined. For policymakers, the use of CIAF is suggested since it provides an estimate of the entire burden of undernutrition.