On December 19, 2014, the Marlins traded Eovaldi, Garrett Jones, and Domingo Germán to the New York Yankees for Martín Prado and David Phelps.

Eovaldi made his first start for the Yankees on April 10, 2015, against the Boston Red Sox, where he pitched ​5 ¹⁄₃ innings, allowing two runs on eight hits.
He was credited with a no decision as the Yankees lost to the Red Sox, 6–5 in 19 innings.
Eovaldi developed a split-finger fastball, which led to improved results.
From June 20 through August 24, Eovaldi pitched to an 8–0 record with a 2.93 ERA.
In September, Eovaldi experienced elbow inflammation, ending his regular season.
For the 2015 Yankees, Eovaldi went 14–3 with a 4.20 ERA, pitching ​154 ¹⁄₃ innings in 27 starts.
Eovaldi was prepared to pitch in the ALDS, but the Yankees were eliminated in the Wild Card Game.

On August 16, 2016, it was announced that Eovaldi would miss the remainder of the 2016 season due to a torn flexor tendon and partially-torn ulnar collateral ligament in his pitching (right) elbow.
Several days later, the Yankees announced that Eovaldi had undergone his second Tommy John surgery.
With the 2016 Yankees, Eovaldi made 24 appearances (21 starts), registering a 9–8 record with 4.76 ERA in ​124 ²⁄₃ innings pitched.
He was expected to miss the 2017 season, after which he would have become eligible for free agency.
On November 23, the Yankees released Eovaldi.
On December 19, 2014, the Marlins traded Eovaldi, Garrett Jones, and Domingo Germán to the New York Yankees for Martín Prado and David Phelps.
Eovaldi made his first start for the Yankees on April 10, 2015, against the Boston Red Sox, where he pitched ​5 ¹⁄₃ innings, allowing two runs on eight hits. He was credited with a no decision as the Yankees lost to the Red Sox, 6–5 in 19 innings. Eovaldi developed a split-finger fastball, which led to improved results. From June 20 through August 24, Eovaldi pitched to an 8–0 record with a 2.93 ERA. In September, Eovaldi experienced elbow inflammation, ending his regular season. For the 2015 Yankees, Eovaldi went 14–3 with a 4.20 ERA, pitching ​154 ¹⁄₃ innings in 27 starts. Eovaldi was prepared to pitch in the ALDS, but the Yankees were eliminated in the Wild Card Game.
On August 16, 2016, it was announced that Eovaldi would miss the remainder of the 2016 season due to a torn flexor tendon and partially-torn ulnar collateral ligament in his pitching (right) elbow. Several days later, the Yankees announced that Eovaldi had undergone his second Tommy John surgery. With the 2016 Yankees, Eovaldi made 24 appearances (21 starts), registering a 9–8 record with 4.76 ERA in ​124 ²⁄₃ innings pitched. He was expected to miss the 2017 season, after which he would have become eligible for free agency. On November 23, the Yankees released Eovaldi.
Nathan Eovaldi