After playing for semi-professional side Dunkerque, Issa started his professional career with Marseille in 1995 and went on to play in the 1999 UEFA Cup Final. He moved to Chelsea on loan in January 2001, although he did not play a competitive game for the London club. He is best known in England for his spell with Watford in 2001–02. Signed by new manager Gianluca Vialli from Marseille, Issa scored once, against Portsmouth. Issa was memorably dropped by his stretcher bearers after an injury in a home game against Birmingham City, and was put on the club's transfer list on 14 February 2002, only five months after he had signed for the club. He never played for Watford again, but played for his country at 2002 FIFA World Cup whilst still contracted to Watford.
After leaving Watford, Issa signed for Olympic Beirut and won both Lebanese Premier League and Lebanese FA Cup in his first season with the club, but was released in the 2004–05 season as the club's ownership was changed due to financial considerations. He signed for Ionikos of Greece and later for OFI Crete, also in Greece, where he stayed until 2009.