In July 2003, Agius was part of the Sliema Wanderers under-16 squad that participated in the Nikola Kotkov Tournament, organised by the Academy Lokomotiv 101.

In February 2006, Agius featured in the Torneo Mondiale di Calcio Coppa Carnevale and scored two goals, one against Pistoiese and the other against Torino.

His performances with Virtus earned him a four-year contract with Messina in March 2008 but the following summer, financial difficulties forced the Serie B club to file for bankruptcy.

On 31 August 2011, Agius signed for Italian side Latina, and was part of the squad that won promotion to Serie B as well as winning the 2012–13 Coppa Italia Lega Pro.

US Latina's promotion to the second division of Italian football led to a squad overhaul in the summer of 2013 and Agius opted to join Sardinian club Torres.

Agius was also in the Hibs team that caused a shock by beating Israel's Maccabi Tel Aviv 2–1 in the first leg of their 2015–16 UEFA Champions League second qualifying round tie at the Hibernians Stadium on 14 July 2015.