Jinja City was found in 1901 by British settlers and it was planned under colonial rule under the leadership of Ernst May a German architect and urban planner in 1948. Ernst May also designed an urban planning scheme of Kampala which he later called “neighborhood units’’. Estates were built for the ruling elites and so many slums were cleared leading to displacement of many people in 1950s. in 1954, the construction of Owen Falls Dam submerged the Ripon Falls. The Flat Rocks that gave the area “Jinja” its name disappeared under water as well. The local Baganda called the place Mayinja which means a place of stones and this is where the Jinja derives its name from.

Jinja was among the Ugandan Cities that were affected by the Uganda-Tanzania war of 1978-1979. After the fall of Kampala to the coalition of Tanzania People’s Defence Force (TPDF) and the Uganda National Liberation Army (UNLA), Ugandan President Idi Amin by then flew to Jinja where he rallied the remnants of the Uganda Army (UA) according journalist Bwire Kapo, Amin declared Jinja the new Capital of Uganda but he later flew to Arua and later into exile.

Parts of the local Uganda Army garrison belonging to Eagle Colonel Gaddafi Battalion remained, drunkenly murdering and harassing local civilians, however most of the soldiers deserted and fled Jinja. However on 22 April 1979, Tanzania People’s Defence Force and its Uganda National Liberation Army allies, assaulted Jinja and occupied it after overcoming some resistances. The troops of Uganda Army (UA) and the Jinja’s locals welcomed TPDF (Tanzania People Defence Force) warmly. The operation was accompanied by looting in the City. After the end of hostilities, Tanzanian officers used Jinja as a hub to transport stolen goods from Uganda to Mwanza including war materials.