During his international career, Muscat represented the Australia U-20 side at the 1991 FIFA World Youth Championship in Portugal and the 1993 FIFA World Youth Championship in Australia. He represented the Australia U-23 side at the 1996 Summer Olympics. After making his full international debut for Australia in September 1994 against Kuwait, Muscat represented the national side at the 1997 FIFA Confederations Cup, 2000 OFC Nations Cup, 2001 FIFA Confederations Cup and the 2005 FIFA Confederations Cup.