The Indians traded Frazier (among other prospects) to the New York Yankees in 2016 for relief pitcher Andrew Miller.

In 2014, Frazier played for the Lake County Captains of the Single–A Midwest League where he batted .266 with 13 home runs and 50 RBIs in 120 games.

[12] In 2015, Frazier played for the Lynchburg Hillcats of the High–A Carolina League where he compiled a .285 batting average with 16 home runs and 72 RBIs in 133 games.

[15] On July 31, 2016, the Indians traded Frazier along with Justus Sheffield, Ben Heller and J. P. Feyereisen to the New York Yankees for Andrew Miller.

[23] On July 8, Frazier hit his first career walk-off, a home run off of Corey Knebel, giving the Yankees a 5-3 win over the Milwaukee Brewers.

On July 8, Frazier was once again called up to the Major Leagues as starting center fielder Aaron Hicks was banged up.

[31] On September 5, manager Aaron Boone said that Frazier would miss the rest of the season to get treatment for ongoing symptoms caused by the concussion he suffered earlier in the year.

[33] Frazier was first called up on April 2 in response to the Yankees having three injured outfielders at once: Giancarlo Stanton, Aaron Hicks, and Jacoby Ellsbury.

He hit a go-ahead three-run home run to the left field seats that ultimately gave the Yankees the win.

On June 2, New York trailed Boston 3-2 in the seventh inning when Frazier let Eduardo Núñez’s sharp single get under his glove for a two-base error that allowed Michael Chavis to score from first base.

Three batters later, Frazier dived and missed Andrew Benintendi’s liner, which fell for a single as Brock Holt scored from first.

Then in the eighth, he took a bad route on Chavis’ ball near the right-field line, letting it skip by for an RBI triple as fans booed.

[35] Due to his poor defense and attitude, Frazier was optioned back to the minors on June 16 when the Yankees acquired Edwin Encarnación.

In his first game of the season the next day, Frazier went 3-for-4, including a home run in his first at-bat and a double in the sixth inning.

[45] Frazier cleared waivers and chose to accept a minor-league assignment with the Iowa Cubs of the Pacific Coast League, allowing him to continue to receive his major-league salary.

[47] He was assigned to the Triple-A Round Rock Express to begin the year, where he made 15 appearances and hit .250/.350/.442 with 1 home run and 4 RBI.

[48] On April 28, 2023, Frazier signed a minor league contract with the Chicago White Sox and was assigned to the Triple-A Charlotte Knights.

On June 22, 2022, Frazier told a broadcaster for the Iowa Cubs that he wanted to be called by his middle name, Jackson, moving forward.

[57][58] After using his middle name for a portion of the 2022 season, Frazier claimed that the decision was part of "a joke that just went too far," and thereafter continued to go by Clint.