New York Mets general manager Billy Eppler resigned Thursday, continuing an overhaul of the team’s leadership with the recent hiring of president of baseball operations David Stearns and firing of manager Buck Showalter.

Eppler, 48, was expected to stay on, despite owner Steve Cohen officially handing control of the team’s baseball-operations department to Stearns this week.

He does so after one of the most disappointing seasons in franchise history. The Mets entered the year with the largest payroll in Major League Baseball history and World Series aspirations. They ended it having dealt nearly a quarter of their major league roster at the trade deadline and finishing 75-87, fourth place in the National League East division and 29 games behind first-place Atlanta.

Eppler was hired in late 2021 after the Mets fired Zack Scott, their interim GM, who had been charged with DWI but later was found not guilty. Scott replaced Jared Porter, who was fired 38 days after being hired following an ESPN report that he had sent explicit text messages to a female reporter.

Stearns, 38, joined the Mets after seven seasons running the Milwaukee Brewers that included four playoff appearances. While his arrival in Queens had been long expected, there was no indication in his introductory news conference three days ago that Eppler would not be part of the team’s infrastructure.

Eppler’s first season with the Mets, who he joined after five years as Los Angeles Angels GM, wound up with 101 wins — and an ignominious loss to San Diego in the wild-card round.

While Eppler warranted praise for a 2022 offseason in which he signed ace Max Scherzer and acquired steady starter Chris Bassitt, his lack of urgency at the trade deadline let to a trio of dud moves, as the team added only designated hitter Daniel Vogelbach, first baseman Darin Ruf and outfielder Tyler Naquin.

At the deadline a year earlier, in an ill-fated effort to make the postseason, they had traded outfielder Pete Crow-Armstrong, who would become a top prospect, for infielder Javier Baez.

The Mets’ spending spree this past winter brought back closer Edwin Diaz and centerfielder Brandon Nimmo while adding future Hall of Famer Justin Verlander and Japanese star Kodai Senga to the rotation. Diaz’s season-ending injury in the World Baseball Classic cast a pall on the season, and by the time the deadline rolled around, the Mets punted, trading Scherzer to the Texas Rangers and Verlander to the Houston Astros.

New York enters a seminal winter, with two-way star Shohei Ohtani — whom Eppler signed as GM of the Angels — reaching free agency and the Mets mulling the future of first baseman Pete Alonso, who is a year away from free agency and hired agent Scott Boras this week.

The Mets also will continue looking for a manager after Stearns fired Showalter, who Eppler hired in December 2021, three months into his tenure.