Despite a large new contract offer in Vietnam, he decided to return to the U.S.  Nguyen signed a multi-year deal with Major League Soccer on December 7, 2011 and was originally allocated to the Vancouver Whitecaps FC in a weighted lottery. He made three preseason appearances with Vancouver before being waived on March 1, 2012. On March 2, 2012, he was selected by the New England Revolution with the second overall pick in the MLS Waiver Draft. Nguyen made 30 regular-season appearances for the Revolution in 2012, including 27 starts. He finished second on the team with five goals and was voted the Midnight Riders Man of Year by the fans. His second career MLS goal—and second goal of the game against Vancouver on May 12—was one of four finalists for the MLS Goal of the Year Award. In 2013, Nguyen appeared in 33 league matches, scoring four goals and recording seven assists. In 2014, Nguyen led the Revolution with 18 goals and 5 assists, which is the most ever by a midfielder in an MLS season, and was again voted the Midnight Riders Man of the Year. For his contributions to the team—including 9 game-winning goals in the regular season—Nguyen was named as a finalist for the 2014 version of the Major League Soccer MVP Award along with Seattle Sounders forward Obafemi Martins and Los Angeles Galaxy forward Robbie Keane. Nguyen's goal against the Houston Dynamo also made it to the final round of voting for the 2014 version of the MLS Goal of the Year Award. Nguyen led the team in assists and finished second in scoring during the 2015 season. During the 2016 season, Nguyen became the Revolution's team captain. He led the team in assists, with 10, and finished 3rd in goals scored, with 6. In August 2017, The Revolution reportedly rejected a $1 million bid for Nguyen from Israeli Premier League side Maccabi Haifa. He would finish the 2017 season first in assists, and second in goals scored, with 15 and 11 respectively. Citing frustration over his contract (he was at the time the seventh-highest paid player on the team, making $500,000, despite ranking fifth in the league in over-all goals over the previous four seasons), Nguyen reportedly demanded a trade at the end of the 2017 season on three separate occasions. The dispute would ultimately lead to his sitting-out the team's pre-season training camp. On May 1, 2018, New England traded Nguyen to Los Angeles FC in exchange for $350,000 in General Allocation Money and $350,000 in Targeted Allocation Money.