An effective institutional structure is a crucial tool for having a highly functioning education system and consequently, economic growth and development. We analyse the effects of decentralisation and school autonomy on the quality of education in two MENA countries (Jordan and Tunisia), by using the OECD PISA 2009 database. Results reveal that decentralisation has a positive impact on the quality of education in some decision-making areas, whereas most autonomy related variables are not significant. Accordingly, schools with more autonomy management and facing more competition do not lead to different results than others, while (public) ownership is positively significant only in Tunisia. However, private funding and accountability measures are positively associated with student achievement.