February 2001 saw the formation of the world's first women's professional soccer league in which all the players were paid. Women's United Soccer Association (WUSA) had its inaugural season in 2001. Lilly was the team captain and a founding member of Boston Breakers. In her first season with the team, she appeared in all twenty-one matches and played every minute of the season. She led the league in assists with eleven and added an additional three goals. For her performance, she was named First Team All-WUSA. In 2002, she started in a further nineteen games. She increased her point total for the season, scoring eight goals and assisting on thirteen others. She was again named First Team All-WUSA and was a starter on the WUSA North All-Star Team. In 2003 Lilly started all nineteen games in which she played, chipping in three goals and four assists and again being named to First Team All-WUSA, the only player in the history of the league to do so. Following the 2003 season, the WUSA ceased operations.