Maloney won the Johnny Warren Medal for player of the year in NSL season 1998/99. In season 1999/2000, it was Maloney's growing reputation as the most prolific goalscoring midfielder in the league that prompted the then Chairman of Perth Glory, Nick Tana, to pay an Australian record domestic transfer fee to secure his services from Marconi. This transfer still stands as an Australian record today.
Maloney represented the Australian under 20's which finished fourth at the 1991 FIFA World Youth Championship in Portugal where he played all six games and scored the winning goal against tournament favourites USSR to secure a 1-0 victory. He also competed at the 1992 Summer Olympics in Spain for the Australian Under 23's team which finished fourth. He made several Socceroos appearances between 1998 and 2000. He was an Australian Institute of Sport scholarship holder.