Agius was the captain of his hometown club side Valletta and is one of the most well known and highly respected figures in Maltese football history.

[citation needed] Gilbert Agius has received three Malta Football Association Player of the Year awards.

[5] At the start of the 2007–08 season Agius was on trial with Enköpings SK FK, but later he opted to stay with Valletta.

After his short spell with Xewkija Tigers, Agius came back to Valletta, where he took again the place of assistant manager.

In 2019 he replaced Danilo Doncic as a caretaker manager of the citizens, and led the club to win the title after beating Hibernians in the decider match.

[7] In December 2020 Agius came back in help of his club, taking the role of caretaker coach again after the resignation of Jesmond Zerafa.