Rachel Balkovec is moving on up, but out of the Yankees organization.

After becoming the first woman to manage an affiliated minor league team, leading the Yankees’ Low-A club the past two seasons, Balkovec has agreed to become the Marlins’ director of player development, a source confirmed to The Post on Tuesday. MLB.com first reported the hire.

Balkovec has previously indicated she aspires to be a general manager in the future, so moving from the dugout to a front office position would seem to align with that goal.

The 36-year-old Balkovec joined the Yankees organization in November 2019 as a minor league hitting coach after working as a minor league strength and conditioning coach for the Cardinals and Astros.

She was then promoted to manage Low-A Tampa ahead of the 2022 season.

“In general, I think that I want to be a head coach, and right now I’m obviously in a role where this is a lot of leadership responsibility, but I want all the pressure,” Balkovec told The Post’s Steve Serby in April of 2022.

“So I want to be a head coach, and I think the GM of most baseball teams is somebody who makes maybe more decisions than the major league manager. I’m also interested in the whole organization and not just one team, so just kind of having the bird’s-eye view I guess.”

The Marlins were the first MLB organization to have a female general manager when they hired Kim Ng in 2020, though Ng left the club after last season, reportedly because it wanted to hire a president of baseball operations above her.

The Marlins have since hired former Rays GM Peter Bendix as their new president of baseball operations, and he will now have Balkovec as part of his staff.