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The role of the school principal in South African schools has evolved. No longer are they only seen as managers and administrators; they are also expected to be the standard bearers of teaching and learning activities at the school. South African secondary schools operate in varying socioeconomic conditions, and principals in these contrasting contexts are faced with challenges and tasks that may require differing school leadership and management (SLM) approaches. These challenges must be overcome while striving for quality educational outcomes. Most of the research on SLM and educational outcomes in South Africa is based on small-scale studies and are descriptive in nature. Here, we used data from the 2015 Trends in International Mathematics and Science Study (TIMSS), a nationally representative study of Grade 9 learners and their school environments. Our aims were to compare the characteristics of SLM in no-fee, fee-paying, and independent schools and to determine whether mathematics achievement gaps in different schooling contexts could be explained by the SLM qualities of a school. We measured SLM based on calculated indicators of a) instructional leadership, b) promoting an orderly and supportive environment, and c) the principal’s experience and training. The findings are based on multivariate estimations using self-reports from the principal and two teachers from 292 secondary schools in South Africa. This methodology allowed us to determine the associations (but not any causal relationships) between SLM characteristics and mathematics across schools that are similar in ways such as resourcing or student wealth.