Objective Malnutrition in children pervades all aspects of their health, growth, cognitive and social development and can lead to irreversible and lifelong effects. We examine the prevalence and determinants of malnutrition in children under 5 in the Ghanaian population. Methods Using data from the latest available Ghana Demographic and Health Survey (GDHS), we estimated and compared prevalence of malnutrition in children among the different subgroups of the population. We used multivariable logistic regression to identify potential factors associated with childhood malnutrition in Ghana. Results Overall, 35.6 % (95 % CI: 33.6, 37.6) of Ghanaian children under 5 years of age suffer from some form of malnutrition. Specifically, 27.5 % (95 % CI: 25.1, 28.7), 13.8 % (95 % CI: 12.5, 15.3), 8.9 % (95 % CI: 7.8, 10.2) were stunted, underweight and wasted, respectively. Results from the logistic regression indicate that gender and age of the child, educational and nutritional status of the mother, and financial status of the household are risk factors associated with childhood malnutrition in Ghana. Conclusions for Practice In view of the observed high rate of malnutrition among Ghanaian children despite the interventions that have been in place since the 1990s, there is a need for increased awareness and improved targeted interventions as well as knowledge translation tools including extensive education on infant and young child feeding practices.