The Second Republic of Uganda existed from 1971 to 1979, when Uganda was ruled by Idi Amin's military dictatorship. Amin's rule formally came to an end with the Uganda-Tanzania War, which ended with Tanzania occupying Uganda and Amin fleeing into exile.

The Ugandan economy was devastated by Idi Amin's policies, including the expulsion of Asians, the nationalisation of businesses and industry, and the expansion of the public sector. The real value of salaries and wages collapsed by 90% in less than a decade. The number of people killed as a result of his regime is unknown; estimates from international observers and human rights groups range from 100,000 to 500,000.

From Uganda's independence from Great Britain in 1962 to early 1971, Milton Obote's regime had terrorized, harassed, and tortured people. Frequent food shortages led to food prices experiencing hyper-inflation, with one contributing factor being Obote's persecution of Indian traders. During Obote's regime, flagrant and widespread corruption had emerged. The regime was disliked, particularly in Buganda where people had suffered the most.

By January 1971, Milton Obote, then President of Uganda, was prepared to rid himself of the potential threat posed by Idi Amin. Departing for the 1971 Commonwealth Heads of Government Meeting at Singapore, he relayed orders to loyal Langi officers that Amin and his supporters in the army were to be arrested. Various versions emerged of the way this news was leaked to Amin. Also, the role of the foreign powers in the coup had been debated^{[by whom?]} after the fact. Documents declassified by the British Foreign Office reveal that, contrary to earlier speculations, it was not directly facilitated by Great Britain but benefited from covert support by Israel which saw Idi Amin as an agent to de-stabilise Islamic Sudan. The documents however unveil an outrightly positive assessment of Amin's personality by the British authorities as well as recommendations of support and the sale of arms to the new regime.

In any case, Amin decided to forestall Obote and strike first. In the early morning hours of 25 January 1971, mechanized army units loyal to him attacked strategic targets in Kampala and the airport at Entebbe, where the first shell fired by a pro-Amin tank commander killed two Roman Catholic priests in the airport waiting room. Amin's troops easily overcame the disorganized opposition to the coup, and Amin almost immediately initiated mass executions of Acholi and Langi troops, whom he believed to be pro-Obote.

The Amin coup was warmly welcomed by most of the people of the Buganda kingdom, which Obote had attempted to dismantle. They seemed willing to forget that their new president, Idi Amin, had been the tool of that military suppression. Amin stated intentions about his government's intent to play a mere "caretaker role" until the country could recover sufficiently for civilian rule. Amin repudiated Obote's non-aligned foreign policy, and his government was quickly recognized by Israel, Britain, and the United States. By contrast, presidents Julius Nyerere of Tanzania, Kenneth Kaunda of Zambia, Jomo Kenyatta of Kenya, and the Organization of African Unity (OAU) initially refused to accept the legitimacy of the new military government. Nyerere, in particular, opposed Amin's regime, and he offered hospitality to the exiled Obote, facilitating his attempts to raise a force and return to power.

Amin's military experience, which was virtually his only experience, determined the character of his rule. He renamed Government House "the Command Post", instituted an advisory defence council composed of military commanders, placed military tribunals above the system of civil law, appointed soldiers to top government posts and parastatal agencies, and even informed the newly inducted civilian cabinet ministers that they would be subject to military discipline.

Uganda then became a military dictatorship which was, in effect, governed from a collection of military barracks scattered across the country, where battalion commanders, acting like local warlords, represented the coercive arm of the government. The Ugandan General Service Unit (GSU), an intelligence agency created by the previous government, was disbanded and replaced by the Ugandan State Research Bureau (SRB). SRB headquarters at Nakasero became the scene of torture and executions over the next couple of years.