After beginning his professional career in the Australian National Soccer League with Sunshine George Cross in 1989, Muscat forged a successful, albeit controversial career in the United Kingdom with Crystal Palace, Wolverhampton Wanderers, Rangers and Millwall. He returned to Australia in 2005 to captain Melbourne Victory in the inaugural season of the A-league. Kevin has won 3 titles with Melbourne Victory, and had a very successful year in 2015 winning the A-League title and minor premiership. He later won the FFA cup at the start of 2016.
Muscat retired from professional football in March 2011 after Melbourne Victory's 2011 AFC Champions League campaign, citing his growing frustration at his inability to keep pace with the game. In June 2011 Muscat was reconfirmed as assistant coach at Melbourne Victory. Muscat briefly rejoined his former club Sunshine George Cross for part of the 2011 Victorian State League Division 1 season.
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.