In 2008, the New York Yankees signed four players, including Bañuelos and Alfredo Aceves, from the Mexican League for $450,000. Bañuelos participated in the All-Star Futures Game in 2009. Bañuelos missed some time during the 2010 season with an appendectomy. In 2010, Bañuelos split time between the Class-A AdvancedTampa Yankees and the Class-AA Trenton Thunder. Bañuelos played in the Arizona Fall League after the 2010 season, earning the start in the team's all-star game. Before the 2010 season, he was rated as the Yankees sixth best prospect according to Baseball America, and in 2011 he was rated as the fourth best. He was also one of the top 50 overall prospects according to MLB.com. In 2011, Bañuelos was invited to spring training with the Yankees for the first time. Mariano Rivera said that he believed Bañuelos was the best pitching prospect he had seen. He won the James P. Dawson Award, given annually to the best rookie in camp. He began the 2011 season with Trenton was promoted to the Scranton/Wilkes-Barre Yankees of the Triple-AInternational League on August 2. Bañuelos was again invited to spring training in 2012. After struggling through injuries during the 2012 season, Bañuelos underwent Tommy John surgery, and missed the entire 2013 season. He returned to pitch for Scranton/Wilkes-Barre in 2014.
Atlanta Braves
On January 1, 2015, the Yankees traded Bañuelos to the Atlanta Braves for pitchers David Carpenter and Chasen Shreve. He was invited to spring training, and assigned to the Gwinnett Braves of the International League on March 27. The Braves promoted Bañuelos to the major leagues on July 2, 2015. In his debut that day, he pitched innings and recorded seven strikeouts and no earned runs against the Washington Nationals. He ended the outing by hitting Denard Span and Danny Espinosa and was removed from the game due to cramping and dehydration. Later that month, tests revealed that Bañuelos had a bone spur. He was sent to the minors for rest and rehabilitation, before a second callup in September. The bone spur continued to bother him, and Bañuelos underwent surgery to remove it on September 17. In 2016, Bañuelos contended for a spot in the rotation in spring training. However, on March 22, he began to feel discomfort in his pitching elbow and underwent an MRI that uncovered no irregularities. The team placed Bañuelos in extended spring training until May, when he was cleared to join Gwinnett after a one-game rehab assignment with the low A Rome Braves. On May 23, 2016, he was optioned to Gwinnett. The Braves demoted him to the Mississippi Braves of the Double-A Southern League. Bañuelos was designated for assignment on August 12.
On November 17, 2017, Bañuelos signed a minor league contract with the Los Angeles Dodgers. He was assigned to the Oklahoma City Dodgers of the PCL for the 2018 season and was selected to represent the PCL at the Triple-A All-Star Game and was also selected to the post-season PCL All-Star Team. He made 31 appearances, with 18 starts and posted a 3.73 ERA with nine wins and seven losses.
Chicago White Sox
On November 1, 2018, the Dodgers traded Bañuelos to the Chicago White Sox in exchange for minor league infielder Justin Yurchak. The White Sox added him to the 40 man roster. The White Sox promoted him to the major leagues as a long reliever and spot starter. He gave up nine runs, all of them earned, to the Boston Red Sox in a single inning during a home game on May 4, 2019, exiting the game with a 30.34 ERA. On October 28, the White Sox outrighted Bañuelos off of the roster. He elected free agency following the season.
On February 2, 2020, Bañuelos signed a minor league deal with the Seattle Mariners. Bañuelos was released by the Mariners organization on May 28, 2020.
Fubon Guardians
On June 18, 2020, Bañuelos signed with the Fubon Guardians of the Chinese Professional Baseball League.
