Fagúndez became a regular starter for the New England Revolution in 2013, when he had a successful breakout season, scoring 13 goals and assisting 7. Fagúndez quickly became one of MLS's great young talents, and won player of the week honors in week 14 of the 2013 MLS season. Fagúndez obtained a US green card in October 2013 qualifying him as a domestic player under MLS squad rules. He was featured on an episode of documentary television show that MLS 36 in August 2013. During the 2015 season, Fagúndez became the youngest player in MLS history to reach 100 appearances for his club.
In April 2013, he stated that he would be willing to represent either Uruguay or the United States at the 2013 FIFA U-20 World Cup. However, he was not called up by Uruguay and was not eligible for represent U.S. at the time due to not having citizenship.
Fagúndez received his U.S. green card in October 2013, which qualifies him as a domestic player for MLS roster purposes.