Student activism and politics was a significant part of Ugandan higher education in the 20th century. Beginning in the 1930s, Ugandan universities and secondary schools were a center for revolutionary movement. For three decades, most youth movements focused on independence from the British Empire. Following independence in 1962, activist groups shifted focus internally. Student leadership groups at universities around Uganda, especially Makerere University, were politically affiliated and elections for student government were closely tied to political standing. Student activist groups were key opposition against the regimes of Milton Obote and Idi Amin, and students were especially targeted for persecution during Amin's presidency. During Yoweri Musevini's presidency, students have been leading critics, participating in large protests both preceding and following Musevini's move to eliminate presidential term limits in 2006. Consistent opposition to President Yoweri Musevni culminated in three shutdowns of Makerere University.

The 1950s in Uganda showed a movement towards pan-africanism and independence, supported by the multi-national student bodies of universities like Makerere College and Uganda Christian University. In 1954, students founded the Tanganyika African Welfare Society at Makerere College, designed to promote Tanganyikan independence and fair treatment. The welfare society was considered to be one of the significant student movements of colonial Africa, along with the National Union of Ghana Students.

In the mid-1950s, Abana de Baganda, the student body of Baganda, engaged in tribal protests against the colonial government.

In the immediate aftermath of independence, there was a divide between staff and students over the role that universities would play in the newfound regime. Senior staff, mostly expatriates and British hires, believed the universities had an obligation to be independent. Local staffers, on the other hand, saw universities as a tool to support a nationalist agenda. According to Mahmood Mamdani in University Crisis and Reform: A Reflection on the African Experience, the locals were ultimately successful and the university became politically linked. However, the educated group of young people consisted mostly of social elites. Rather than taking on the progressive movements of other student movements of the time, a survey of Ugandan university students showed political apathy.

Milton Obote was the political leader of Uganda from independence in 1962 until 1971. He served as Prime Minister until 1969, when he assumed absolute power following an assassination attempt. There were minor student clashes with Obote both during his leadership.

In May 1968, students protested an anti-British demonstration after three Rhodesian Africans were hanged.

Later that year, a group of students planned a protest in which they intended to parade in front of British High Commission in protest of arms sales to South Africa. The army stopped the march before it left campus, using tear gas to control them.

In 1969, the president of the student guild was arrested and jailed for inciting an illegal demonstration, resulting in Obote's General Service Unit establishing a spy network within the university.