School effectiveness in areas of social deprivation is a fundamental issue for every society, because it is related to social justice, equity and development, which are important matters for every developed or developing country. Social justice in education means that any student, whatever their social background, has equal access and opportunities to receive an education of quality. It is often considered that schools in the poorest neighbourhoods provide a lower quality of education than institutions in more advantaged areas. Nevertheless, taking into account all the barriers that some schools have to face, there are some institutions that seem to make a difference. They have demonstrated that it is possible to be more successful in terms of educational outcomes, despite the impact of their student intake from disadvantaged backgrounds. This study intends to contribute to the school effectiveness field through the study of effective secondary schools from two important regions in Chile, which are characterised by their disadvantaged student intake. The main aim of this research is to gain greater understanding of the particular characteristics of effective schools in challenging contexts and the influences of these particular features on the students’ academic outcomes. A sample of schools was selected after the analysis of the students’ academic achievement demonstrated in their results in a national examination over a period of 3 years. The sample only considered schools with a student intake characterised by high social vulnerability. These schools were analysed using case studies and a mixed methods research approach. The intention was to explore the school processes that support effectiveness and to generate some illuminating findings, in order to contribute to educational policy and practice.