This study endeavours to make a new contribution to knowledge in the field of mathematical learning in schools in challenging circumstances. By combining quantitative advanced secondary data analysis of International Large-Scale Assessment (ILSA) and a qualitative case study for investigating teaching and learning practices, the study aims to establish a methodological framework and a research design that help to harness TIMSS outcomes for school improvement. Availing of TIMSS (2011) data and applying a mixed-methods research design, the research aimed to find out what value-added Palestinian schools provide in teaching mathematics to their students. Furthermore, and moving beyond TIMSS, the research investigated in-depth the teaching-learning practices to improve mathematics education. The secondary data analysis of TIMSS, by applying the multilevel modelling (MLM) methods, formed the first phase of the study and informed the design of the second phase. School practices and characteristics were compared between schools in Palestine on the basis of association to students’ performance in mathematics. The first phase findings revealed a weak relationship between students’ mathematics performance and school level context, resources, and practices. Nevertheless, students’ background, socioeconomic status (SES), self-concept and attitudes evidenced significantly stronger effects. In the light of the first phase study findings, a second phase was conducted. The second phase involved a qualitative case study of one of the schools that had mitigated for background effects and had students with high performance in mathematics. The case study focused on how the staff articulate the processes and practices that have facilitated the high value-added scores in the TIMSS data. The qualitative phase of the study emphasised and explained how efficient and competent staff at school overcame the challenging circumstances and improved learning. In addition to the important key findings from the two research phases, the current study ultimately suggests future theoretical and methodological frameworks that can be used in research at a national level in Palestine or any education system with similar circumstances.