The purpose of this paper is to study the gender differences in learning achievement by exploring in Southern and Eastern African countries the educational environment and curriculum contents. The study is based on the data archive of a large-scale assessment administered by a consortium known as Southern and Eastern Africa Consortium for Monitoring Educational Quality (SACMEQ) during 2000 and 2007. The examination of the progress in gender equality in various educational dimensions revealed that many countries have improved the gender balance in school participation while the quality issue tended to remain unchanged between 2000 and 2007. However, by comparing the characteristics of groups of schools within two countries, it was suggested that gender differences in achievement may not always be related to the availability of school resources and/or the wealth of the pupils. By examining different domains of reading and mathematics subjects, it seemed that boys tended to do better in the ‘documents’ domain of reading and the ‘measurement’ domain of mathematics while girls tended to do better in the ‘expository’ domain of reading and the ‘number’ domain of mathematics.