The EU programme Improving Secondary Education in Malawi (ISEM I and II) has two main objectives: (1) improving access to secondary education through upgraded, safe school facilities, bursaries and bicycles for Community Day Secondary Schools (CDSS), and (2) improving quality in secondary education through new curriculum, syllabus and materials, and improving teacher training, decentralised school management, and community involvement in school improvement. Between 2016 and 2019, improved access was achieved in the reduction of classroom to student ratios from 1:61 to 1:47, a 31% increase in enrolment: 37% for girls and 24% for boys, and a reduction in dropout from 7.4% to 3.8%. Improved quality was achieved through nearly 6,000 teachers oriented on the new curriculum and continuing professional development (CPD) for all the CDSS supported by the programme. ISEM targets both boys and girls and gender equality is a significant, but not its primary, objective. Nonetheless, ISEM takes a gender transformative approach to target girls’ access to secondary education in predominantly rural areas of Malawi, using a combination of gender mainstreaming and gender targeted initiatives to effect change within schools, school systems, and the community.