According to section 29(e)(iii) of the Refugees Act, a recognized refugee shall receive at least the same treatment as aliens generally in similar circumstances regarding access to secondary education. The wording of the provision consistent with the lower threshold of Article 22 of the Refugee Convention (1951) that provides that States should accord refugees treatment as favorable as possible, and, in any event, not less favorable than that accorded to aliens generally in the same circumstances. Hence, refugees are entitled to the same treatment as any other non-nationals in the same circumstances. However, subsidiary legislations or education related policies have not expounded on the meaning and implications of the phrase “aliens generally in similar circumstances”.

According to Section 10(1) of the Education Act, there is a four-tier model: pre-primary; primary; post primary and training; and tertiary education. The secondary education level consists of four years of lower and two years of advanced level of secondary education.  In 2007, the Government of Uganda has introduced the Universal Secondary Education (USE) that aimed at opening the access and opportunities for poor students by providing free access to secondary education for nationals. The application of the Refugees Act excludes refugees from benefiting from such policy. The Government provides a grant for each child to the participating secondary schools and the grants are not available to schools for refugee children. However, the Government maintains that, in practice, refugees enjoy fee access to the program. 

According to the Gap Analysis conducted in 2021 by the Second Education Response Plan for Refugees and Host Communities in Uganda 2021/22-2024/25, prepared by the Ministry of Education and Sports , the secondary GER for refugees was 12.1 per cent compared to 9.9 per cent for nationals in the 37 refugee-hosting districts. Compared with a 2017 data, this represented a 0.8 per cent increase for refugees and an 8.0 per cent decrease for nationals. Both the GER for refugees and nationals in refugee-hosting areas remains significantly lower than the national secondary GER of 25 per cent. As regards gender, girls are experiencing significant challenges to accessing secondary education compared to boys. GER for refugee girls was 7.5 per cent compared to 16.9 per cent for refugee boys, equating to a Gender Parity Index (GPI) of 0.45. The situation is similar for nationals in refugee-hosting districts, with GER for girls at only 8.7 per cent, compared to 11.2 per cent for boys, equating to a GPI of 0.78. NER for refugees and nationals stood at 7.4 per cent and 7.3 per cent respectively. The Education Dashboard reveals that, in the first quarter of 2023, the enrollment rate in secondary school for Congolese refugees is 6%; South Sudanese is 12% and; other refugees is 5%.