Introduction: Prevalence of malnourished children in Putrajaya was unexpectedly high in 2016. This paper describes the study protocol for a case-control study conducted to identify the associated factors of malnutrition among children under 5 years old in Putrajaya. Methods: This study involved two phases. Phase I was ‘screening’ where all children aged 6-59 months in 118 preschools and four government health clinics were measured for their weight and height. The World Health Organization Anthro software was used to determine the nutritional status of these children. Phase II was the ‘interview’ where children from screening were sampled into four pairs of case and control. The optimum sample size for the case of stunted, wasted, underweight, and overweight were 380, 335, 318, and 308, respectively. The same number of controls were recruited. Parents/caregivers of selected children were approached to obtain data on parental factors, children factors, food intake factors, and environmental factors that contributed to malnutrition. Data analysis was performed by multiple logistic regression in SPSS version 26. Results: Screening phase successfully measured 8,261 (50.1%) children from an estimated 16,500 children under 5 years old in Putrajaya. The number of children who were stunted, wasted, underweight, and overweight were 2,105 (25.5%), 512 (6.2%), 1,516 (18.4%), and 248 (3.0%), respectively. As overweight was undersampled, the number of controls for overweight was doubled to increase the power of the study. Parents/caregivers of selected cases and controls were interviewed in their household or any other venues at their convenience. Conclusion: This protocol promises beneficial outputs to stakeholders and policy makers that can be used for combating malnutrition in children.