From 1991 until 1992, Wakikona served as the Chief Licensing & Flight Inspection Officer for the
Civil Aviation Authority of Uganda. From 1993 until 1998, he served as the
Director of the East African Civil Aviation Academy, also known as the Soroti Flying School, in
Soroti,
Eastern Uganda. From 1999 until 2000, he served as the
General Manager of
Uganda Air Cargo, a government-owned cargo airline. In 2001, he joined politics, contesting the parliamentary seat of Manjiya County in
Bududa District. He won, and was re-elected in 2006 and again in 2011. On 1 June 2006, he was appointed State Minister for Northern Uganda in the Office of the Prime Minister, In the run-up to the 2016 general election, Wakikona was defeated by John Baptist Nambeshe in the
National Resistance Movement primary for Manjiya County, and consequently he did not contest the election. Following the election, in June 2016 Wakikona was replaced as State Minister for Trade by
Michael Werikhe Kafabusa. ==Personal life==