Many education systems within sub-Saharan Africa are affected by the problem of over-aged learners. Children who are above the expected age for their grade experience poorer outcomes relative to other learners and it is therefore of interest to policymakers to accurately identify them for the purposes of informing effective remedial interventions. UNICEF's sixth round of Multiple Indicator Cluster Survey's [MICS6] are among the relatively few robust nationally representative data sources that can be used to calculate the share of over-age for grade learners within education systems. This paper identifies variability in the estimation method used to identify the same target over-age population (i.e. learners who are older than the official age for the grade they are currently attending) across MICS6 country reports in 14 countries in sub-Saharan Africa. Nine countries utilise a different method which captures only part of the desired target population. This approach fails to identify at least 50% of learners who are over-age for grade by two years in their primary education system and up to 57% of over-age for grade learners in lower secondary. Results are discussed in terms of their implications for supporting policymakers to plan and implement effective school-based education and health interventions, using Comprehensive Sexuality Education as an example.