The park is located in the Virunga Mountains and is contiguous with the Volcanoes National Park in Rwanda and the Virunga National Park in the Democratic Republic of the Congo. Mgahinga is situated about 15 kilometres (9.3 mi), by road, south of the town of Kisoro and approximately 55 kilometres (34 mi), by road, west of Kabale, the largest city in the sub-region. The entire park is located in Bufumbira County, in Kisoro District. The coordinates of the park are:01 22S, 29 39E (Latitude:1.3650; Longitude:29.6500).
Mgahinga is one of two locations in Uganda in which mountain gorillas can be found; the other being Bwindi Impenetrable National Park. The park has one habituated gorilla group, although this group sometimes crosses the border into Rwanda, which means Mgahinga is not a reliable spot for viewing gorillas.
The park is contiguous with Virunga National Park in the Democratic Republic of the Congo to the west and with Volcanoes National Park in the Republic of Rwanda to the south. The three parks, together form the 434 square kilometres (168 sq mi) Virunga Conservation Area (VCA). At 33.7 square kilometres (13.0 sq mi), Mgahinga forms only about 8% of the VCA. Each country is responsible for protecting its own portion of the VCA.
The national park also covers three of the eight Virunga volcanoes: Mount Muhabura, Mount Gahinga and Mount Sabyinyo, all of which lie on the Uganda/Rwanda border. Any of these can be climbed in one day from the park headquarters.