Lee signed a three-year guaranteed contract with the Timberwolves, rare for a second round pick.[7] After his knee grew sore during training camp, Lee missed the beginning of the 2011–12 season after undergoing surgery to repair a torn meniscus in his left knee.[4][8] On February 6, 2012, he was assigned to the Sioux Falls Skyforce in the NBA Development League to rehabilitate his knee, and he was recalled after playing three games.[9][10] He was reassigned to Sioux Falls on February 29.[11] He made his NBA regular season debut on March 10, 2012.[12]
In 2012–13, Lee missed the majority of training camp and the exhibition season with an injured groin. He started 12 games during the regular season, including a career-high 10 points on December 4, 2012, in a win at Philadelphia. He became slowed by injuries, missing the remainder of the season after two surgeries in January: one hip surgery and another to repair damaged cartilage in his right knee.[13]
On June 27, 2013, the day of the 2013 NBA draft, Lee was traded to the Golden State Warriors, who subsequently traded him to the Phoenix Suns.[14] He spent the summer in Phoenix rehabilitating, but a less than full-strength right quadriceps prevented him from being cleared for full work.[15] He was traded again on October 25, 2013, along with Marcin Gortat, Shannon Brown, and Kendall Marshall, to the Washington Wizards in exchange for Emeka Okafor and a 2014 lottery protected first round draft pick.[16] Lee, Brown, and Marshall were all waived by the Wizards three days later.[17]
On October 7, 2014, Lee signed with the Philadelphia 76ers.[18] However, he was later waived by the 76ers on October 25, 2014.[19] On November 3, 2014, he was acquired by the Delaware 87ers as an affiliate player.[20] On December 5, he re-signed with the 76ers.[21] Six days later, he was waived by the 76ers when they acquired Andrei Kirilenko and Jorge Gutiérrez in a trade.[22] On December 13, he returned to Delaware and played that same night against the Canton Charge.[23] On January 30, 2015, Lee was traded to the Grand Rapids Drive for the returning player rights to Khalif Wyatt.[24]
On November 1, 2017, Lee signed with Igokea for the rest of the 2017–18 season.[28] On January 16, 2018, he left with Igokea,[29] and signed with German club Tigers Tübingen for the rest of the 2017–18 BBL season.[30]
On January 31, 2019, Lee moved to Greece and signed with Kolossos Rodou. On October 11, 2019, he signed with another Greek team, Rethymno Cretan Kings, for the 2019–2020 season, replacing Prince Williams. Lee averaged 5.7 points, 4.8 rebounds, and 2.2 assists per game. On August 16, 2020, he signed with CSO Voluntari of the Liga Națională.[31] After averaging 10.2 points, 4.2 rebounds, and 2.3 assists per game, Lee re-signed with the team on June 27, 2021.[32]
^Krawczynski, Jon (February 14, 2012). "Wolves recall G Malcolm Lee from D League assignment; rookie from UCLA yet to play in NBA". The Washington Post. Associated Press. Archived from the original on February 16, 2012. Retrieved February 16, 2012. The Minnesota recalled rookie Malcolm Lee from their NBA Developmental League affiliate on Tuesday, but anxious Timberwolves fans hoping he is the answer to the team's woes at shooting guard will have to be patient.