In the
2005 WNBA draft, Mahoney was selected in the third round (34th overall) by the
Connecticut Sun. A torn Achilles during the Big 12 championship game her senior season prevented her from playing with the Sun during the 2005 season. Mahoney signed with
Haukar of the Icelandic
Úrvalsdeild kvenna in January 2006, replacing
KeKe Tardy. In nine regular season games, she averaged 27.9 points and 13.1 rebounds per game, helping the team achieve the best record in the league. In the playoffs, Mahoney averaged 28.3 points and 14.3 rebounds. In the finals she broke
Penny Peppas' scoring record by averaging 32.0 points and helped Haukar to a three-game sweep of
Keflavík. For her effort she was named the
Úrvalsdeild Playoffs MVP and the
Úrvalsdeild Foreign Player of the Year. In February 2006, Mahoney signed a three-year contract with the Connecticut Sun. On April 29, 2008, Mahoney was waived by the Comets. In 2006 and in 2007, Megan played in Italy with Parma and the next year, she started to play with
Cras Basket Taranto and she won the Italian title in 2008/2009 2009/2010 (MVP of the finals) 2011/2012 In 2010–2011, during the Euroleague Women, Mahoney was called in the "Rest of World" team against the Representatives of Europe. She scored eight points in five minutes. Between 2014 and 2016, Mahoney played in France for
ESB Villeneuve-d'Ascq. She won the
EuroCup Women 2015 and was runner-up the following season, and also came second in the 2014–15
Ligue Féminine de Basketball. Mahoney signed with San Martino di Lupari of the
Italian Serie A1. On January 15, 2017, she tore her anterior cruciate ligament of the right knee and missed the rest of the season. In May, 2017, Mahoney re-signed with San Martion for the 2017–2018 season. Mahoney had planned to play the 2018–2019 season in Belgium, but tore a tendon in her foot prior to the start of the season. The injury required a surgery and six to eight months of rehabbing. In June 2019, Mahoney announced her retirement from basketball. ==Titles and awards==