Cooper began his career in the youth ranks of Panama’s Árabe Unido. In 2006, he debuted for the professional side, and went on to help the team to achieve various domestic titles in the Liga Panameña de Fútbol. During January 2011 it was reported that Major League Soccer side New York Red Bulls were interested in signing Cooper. However, the transfer did not go through.

He made his debut with the full national team on 7 October 2006 against the national team of El Salvador. On 16 January 2011, he scored his first goal for Panama in a 2–0 victory over Nicaragua in a 2011 Copa Centroamericana match played at Estadio Rommel Fernández in Panama City.

Cooper was part of the Panama U-20 squad that participated in the 2007 U-20 World Cup held in Canada.

In July 2011, he signed with Godoy Cruz of the Argentine First Division.

In February 2015, Cooper joined 2. Bundesliga side FC St. Pauli, only to return to Árabe Unido in September 2015 after playing a mere 125 minutes for the German club.

Cooper was loaned to Major League Soccer side Toronto FC on 18 August 2016. He scored his first goal with Toronto FC on 30 November as Toronto FC beat Montreal Impact 7–5 on aggregate to advance to the 2016 MLS Cup Final.

After the 2016 MLS Cup Playoffs, Cooper signed full-time with Toronto FC.

On 14 December 2017, Cooper’s contract option was declined by Toronto, and he subsequently left the club.

In May 2018, he was named in Panama’s preliminary 35 man squad for the 2018 World Cup in Russia.