Makhanya is a surname. Notable people with the surname include:

Sibusisiwe Violet Makhanya (1894–1971), first black South African social worker Joseph Makhanya (born 1981), South African footballer Leonard Makhanya (born 1964), Swazi boxer Mapaseka Makhanya (born 1985), South African middle and long-distance runner Mondli Makhanya, South African journalist Sibonelo Makhanya (born 1996), South African cricketer Thoko Remigia Makhanya, South African anti-apartheid activist, environmental advocate and poet

See also Makhanya v Minister of Finance