Agius started his career with Santa Lucia, his hometown club, but it was not long before his talent caught the eye of Sliema Wanderers.
In July 2003, Agius was part of the Sliema U-16 team that participated in the Nikola Kotkov Tournament, organised by the Academy Lokomotiv 101.
On December 19, 2003, he made his senior debut for Sliema in a Premier League match against rivals Floriana.
Within a few weeks of making his appearance for Sliema, Agius left for his first overseas challenge. At the age of 16, Agius joined Serbian first-division club FC Zemun. Agius was given a six-month contract to play for Zemun’s youth team, scoring two goals in the process. That summer, Agius was on the move again, this time to Italy where Sicilian club Sporting Mascalucia, who play in the Italian Football League Eccellenza, had agreed to sign him. In his first season with Sporting Mascalucia, Agius scored three goals and was named as the most promising midfielder in the regiomal league. After another positive campaign with FC Mascalucia, in the summer of 2005, Agius secured a contract with then Italian Serie A club Messina where he became a member of their youth squad. In his first year with Messina, Agius was converted into a defender. In February 2006, Agius took part in the 58th Torneo Mondiale di Calcio Coppa Carnevale and scored two goals, one against Pistoiese and the other against Torino. In May 2006, Agius was among the Messina substitutes for the Serie A match against Empoli. After his initial one-year spell with Messina, Agius was loaned to Serie C1 side FC Martina Franca on the last day of the 2006 August transfer window.
During season 2006–07, Agius faced competition for first-team places from experienced and seasoned players but still managed five appearances for FC Martina Franca in the Coppa Italia. In the 2007–08 season, Agius made a return to Serie C2 where he linked up with FC Igea Virtus (Messina), regarded as the second team of Messina Calcio. In his first season with Igea Virtus, Agius played 34 league matches and one in the Coppa Italia. Agius was offered a long-term contract by Messina. In March 2008, Agius signed a four-year deal with Messina but in the summer of 2009, financial difficulties forced the Serie B club to file for bankruptcy. Agius was freed from his contractual obligations with the club. He rejoined Igea Virtus where he was an automatic choice in their first team.
Later in the 09/10 season, Agius joined Serie C team SS Cassino.
In January 2010 Agius was loaned to A.S. Melfi, and then in August 2010 Agius signed a two year contract with A.S. Melfi. He returned to Malta Birkirkara on loan in January 2011.[2] On 31 August 2011 Agius signed with Italian Lega Pro Prima Divisione side U.S. Latina Calcio, who have been promoted.[3][4]