During a match against Washington State University on October 5, she suffered her first season-ending anterior cruciate ligament (ACL) injury.
After taking her time to recover from her second ACL injury, Rapinoe returned for the 2008 season and was on the starting lineup in all 22 games for the Pilots.
She scored her first two goals on October 1, 2006, during a friendly match against Taiwan.
Upon her return to the team in 2009, she led the team in points with five, including two goals and one assist.
Of the signing, Sounders head coach Michelle French said, "Stemming from her leadership and success at the University of Portland, Megan has continued to evolve and grow into one of the most exciting, unpredictable, creative, and flashy players in the women's game." In January 2013, Rapinoe signed for six months with Olympique Lyonnais, the French side that had previously won six consecutive French league championships and two straight European titles, for a reported 11,000 euros (or approximately ,000) a month.Rapinoe trained with the United States women's national soccer team for the first time during the team's 2006 Residency Training Camp in Carson, California.She made her debut for the senior team on July 23, 2006, during a friendly match against Ireland.During the US Youth Soccer National Championships, she scored an equalizer goal in the 18th minute to tie the game 1–1 against the Peachtree City Lazers.Elk Grove United finished second at the nationals after the Lazers scored a game-winning goal in the second half.Rapinoe is an advocate for numerous LGBT organizations, including the Gay, Lesbian & Straight Education Network (GLSEN) and Athlete Ally.In 2013, she was awarded the board of directors Award by the Los Angeles Gay and Lesbian Center.In 2005, as a freshman, Rapinoe helped the Pilots to an undefeated season and the NCAA Division I Women's Soccer Championship.During the College Cup quarterfinal against Notre Dame, she scored twice and served one assist, helping the Pilots win 3–1 and advance to the College Cup.Rapinoe and her sister both attended the University of Portland in Portland, Oregon.The Rapinoe twins almost committed to Santa Clara University before choosing to play for the Portland Pilots on full scholarships.