Sub-Saharan African countries have made remarkable strides in closing the gender gap in primary enrolment and more girls than ever are attending school. With the existing gender differentials in youth literacy rates, an important question is whether they are learning as well as their male classmates. This article explored factors that contribute to gender gaps in reading for sixth-grade pupils from 61 396 pupils from 15 countries in the third evaluation of the Southern and Eastern Africa Consortium for Monitoring Educational Quality (SACMEQ III). Within-class sex differences in test score performance are estimated using ordinary least squares regression models. This is done by analysing the factors associated with female learning that inhibit school attendance and class participation. The results show a female disadvantage in reading in a little under half of the countries studied, which differs from the consistently observed female reading advantage in other parts of the world. Factors that prevent girls from fully attending and participating in school such as domestic responsibilities and hostile school environments explain part of the female disadvantage in reading, indicating that households and schools need to ensure that girls can attend and participate fully in their classes without distractions or fear.