In June 2007, Sekagya signed a three-year contract with Red Bull Salzburg, the then current champions of the Austrian Bundesliga.

He quickly established himself as a regular with the club and finished his first season with 34 Bundesliga appearances to his name, scoring three goals in the league.

[3] On 4 August 2013 Sekagya made his debut for New York starting as a defensive midfielder in a 3–2 victory over Sporting Kansas City.

[4][5] However, Sekagya's giveaway led to an equalizer in Houston's 2–1 victory that knocked New York out of the 2013 MLS Cup Playoffs.

[6] During the 2014 season Sekagya became a regular starter for New York helping the club reach the MLS Cup playoffs.