He was added to the Twins 40-man roster on November 20, 2013. Vargas started the 2014 season with the Double-A New Britain Rock Cats. In July he played in the All-Star Futures Game. Vargas made his MLB debut on August 1, 2014, and hit his first career home run off Jesse Hahn five days later, on August 6, leading the Twins to a 3-1 victory over the Padres. Vargas wound up finishing the season as the Twins designated hitter, hitting 9 home runs with 38 rbi's in 53 games. In the 2015 season, Vargas began the season as the Twins designated hitter although he was sent down a month later after a poor start. He was called up later in the season. Vargas finished his 2015 season with a .240 AVG in 58 games. Vargas was named the American League's Player of the Week for the week of July 4 to July 10, 2016. After excelling at the AAA level, Vargas was given another shot for extended playing time for the Twins. He split time between designated hitter and first base. He finished with a .230 AVG in 47 games with 10 home runs. In 2017, Vargas started the season in Triple A, but was once again called up at the end of April. In the offseason he trained alongside former major League players Carlos Delgado, José ‘Tony’ Valentín, and Manny Ramírez. He also played again with the Indios de Mayagüez in the Liga de Béisbol Profesional Roberto Clemente, Puerto Rico's baseball professional league. On March 16, 2018, Vargas was designated for assignment by the Twins. On March 22, Vargas was claimed off waivers by the Cincinnati Reds. On March 24, the Twins re-acquired Vargas by claiming him off waivers from the Reds, without Vargas appearing in an MLB game with the Reds. He was outrighted to AAA Rochester to start the 2018 season. Vargas elected free agency on November 2, 2018. On November 6, 2018, Vargas signed with the Chiba Lotte Marines of Nippon Professional Baseball (NPB). On November 30, Marines announced that team would not sign Vargas for the next season. Two days later, he became a free agent. On January 27, 2020, Vargas signed a minor-league contract with the Detroit Tigers. Vargas played for the Puerto Rico national baseball team in the 2017 World Baseball Classic where he won a silver medal.