Terms of the deal were not disclosed per team policy.
Lilly captained of the first version of the Breakers during WUSA's three season in 2001-03.
"Kristine is and always will be a Boston Breaker," said Breakers President and General Manager Joe Cummings. "We are delighted to have her back playing with us, and I am sure our fans will be thrilled to see her in a Breakers uniform once again."
"It is great to sign with the Boston Breakers again," said Lilly, who will also be reunited with Breakers head coach Tony DiCicco, whom she used to play for with the U.S. national team. "I am looking forward not only to being a part of WPS, but also to having a professional women's sports team back as a part of the Boston sports scene. I am excited to be on the field playing after having a baby last year, and I am also looking forward to playing in front of our fans and for Tony once again."
Lilly scored 129 goals for the USA. She took the majority of 2008 off from soccer because of the birth of her first daughter, Sidney, in June and missed the team's Olympic triumph in China. But she returned to the national team for a pair of matches in December against China.
As a 20-year-old, she was a member of the U.S. team that won the title at the first ever FIFA Women's World Cup in China in 1991. She was also part of the 1999 World Cup triumph, and won gold medals at the 1996 and 2004 Olympics.