[3] After his sophomore year, he was selected by the New York Yankees in the 18th round of the 2017 Major League Baseball draft, and he signed with the team.

[8] He did not play a minor league game in 2020 due to the cancellation of the season caused by the COVID-19 pandemic alongside still recovering from surgery.

[11] On April 4, 2021, Whitlock made his MLB debut in relief against the Baltimore Orioles, striking out five batters and allowing no runs in 3+1⁄3 innings pitched.

[13] On June 15, Whitlock batted in an interleague game and recorded his first career hit, a single off of Atlanta Braves reliever Edgar Santana.

[17][18] In the postseason, he made five relief appearances, earning one win and allowing two runs in 8+1⁄3 innings as the Red Sox advanced to the American League Championship Series.

[18] Whitlock began the 2023 season on a rehab assignment with the Worcester Red Sox,[23] and was activated by Boston on April 11.

On May 30, 2024, Whitlock underwent an internal brace procedure to repair a torn ulnar collateral ligament, which ended his season.