He started playing football with Kampala City Council in 1998. He went to Argentina, where he played for Atletico Rafaela (2nd division) and for Ferro Carril Oeste (3rd division). His last club in Argentina was Arsenal de Sarandí(Primera División) where he played two seasons. 2007 he was transferred to Europe for 1 million €, what made him the most expensive player from Uganda. He signed for three years and soon became a regular player for FC Red Bull Salzburg.
Sekagya also plays for the Ugandan national football team and is the team's captain.