Liz Benn, the Mets’ highest-ranking woman in baseball operations, is leaving the club, effective after the season, The Post has learned.

The departure of Benn, who has been the Mets’ director of Major League operations the past three seasons, is part of a front-office overhaul orchestrated by David Stearns as he is in the midst of completing his first season as president of baseball operations.

Benn previously had worked for MLB from 2017 until her hiring by the Mets.

Stearns, after a period of evaluation, is now more clearly putting an imprint on his department as he wraps up his first season in charge of the team.

It was learned recently that Stearns already had informed a series of staff they were not being brought back, including director of international scouting Steve Barningham and long-time scouts Ash Lawson and Rudy Terrasas.