Background Childhood malnutrition contributes to nearly half (45%) of all deaths among children under 5 globally. The United Nations’ Sustainable Development Goals (SDGs) aims to end all forms of malnutrition by 2030; however, measuring progress towards these goals is challenging, particularly in countries with emerging economies where nationally-representative data are limited. The primary objective of this study was to estimate the overall burden of childhood malnutrition in Ghana at national and regional levels using 3 data sources. Methods Using data from the long-standing Ghana Demographic and Health Surveys (GDHS), Ghana Multiple Indicator Cluster Survey (GMICS), and the emerging Ghana Socioeconomic Panel Survey (GSPS), we compared the prevalence of malnutrition using the extended composite index of anthropometric failure (eCIAF) for the period 2008-2011. This study included data for children aged 6-59 months and calculated all anthropometric z-scores based on the World Health Organization (WHO) Growth Standards. We tested for differences in malnutrition subtypes using two-group configural frequency analysis (CFA). Results Of the 10 281 children (6532 from GMICS, 2141 from GDHS and 1608 from GSPS) included in the study, the only demographic difference observed was the children included in the GSPS were slightly older than those included in the GDHS and GMICS (median age of 36 vs 30 vs 33 months, P < .001). Based on the eCIAF, the overall prevalence of malnutrition at the national level was higher among children in the GSPS (57.3%, 95% CI: 53.9%–60.6%), followed by the GDHS (39.7%, 95% CI: 37.0%–42.5%), and then those in the GMICS (31.2%, 95% CI: 29.3%–33.1%). The two-group CFA showed that the 3 data sources also estimated different prevalence rates for most of the malnutrition subtypes included in the eCIAF. Conclusion Depending on the data source adopted, our estimates of eCIAF showed that between one-third and half of all Ghanaian children aged 6-59 months had at least one form of malnutrition over the period 2008-2011. These eCIAF estimates should complement the commonly reported measures such as stunting and wasting when interpreting the severity of malnutrition in the country to inform policy decisions.