The Mets’ flirtation with Theo Epstein was short-lived.

In the team’s search for a new president of baseball operations, owner Steve Cohen spoke with Epstein and mutual agreement was reached that it wasn’t the right fit, according to an industry source. The Post reported Tuesday the two sides planned to meet.

The 47-year-old Epstein, who guided the Red Sox and Cubs to curse-busting World Series titles — he has three championship rings in total — was free to speak with the Mets without needing permission (he serves as a consultant for MLB).

Epstein’s contentment working to improve baseball’s on-field product for the league, plus a desire for his next team job to involve an ownership stake, building an organization from the ground up, may have made his candidacy with the Mets a long shot.

Last offseason he departed the Cubs with one-year remaining on a contract that paid him in the neighborhood of $10 million annually. Epstein received that deal after building a team that won the 2016 World Series, the franchise’s first championship in 108 years. With the Red Sox, he presided over World Series winners in 2004 and ’07 — the first of those titles snapped an 86-year drought for the franchise.

Epstein’s removal from the mix could turn Cohen’s full attention toward Billy Beane, who is under contract with Oakland, meaning the Mets would need permission to speak with him.

The 59-year-old Beane — he of “Moneyball” fame — began his post-playing career as a scout with Oakland, hired by then-general manager Sandy Alderson. Beane became the team’s GM in 1997, and the Athletics have reached the postseason 11 times since then, albeit without a World Series appearance. Though there is skepticism within the industry that Beane would leave a comfortable job (as executive vice president he also has an ownership stake in the team estimated to be worth about $40 million), the Mets and Cohen’s deep pockets might represent his best chance to win a championship. Beane was a first-round draft pick by the Mets in 1980.

Beane and Alderson remain tight — the latter was hired as a consultant with Oakland for two seasons before returning to the Mets as team president last offseason. Alderson, who turns 74 in November, has another year remaining on his contract and has indicated a desire to devote his energy toward running the business side of the organization. But Beane’s hiring would likely allow Alderson to stay more involved in a baseball advisory role.

If Beane remains in Oakland, the Mets could turn toward Milwaukee’s David Stearns, but would need permission to speak with him — his contract with the Brewers runs through 2022 — and that likely wouldn’t be sought until after the team is finished with the postseason. Stearns, who grew up a Mets fan in Manhattan and interned for the team, was on Alderson’s radar last offseason, but the Brewers never granted permission for an interview. Could that change this time around? The 36-year-old Stearns will be a hot commodity if he reaches free agency next offseason and perhaps the Brewers would be willing to swing a trade.

Beyond Beane and Stearns, the Dodgers’ Josh Byrnes and Twins’ Derek Falvey could be in play. Last offseason Alderson ultimately took on the responsibility of leading the front office after failing to find a suitable candidate. Alderson hired Jared Porter as general manager, but that union lasted only a month. Porter was fired in January for sexual harassment of a female reporter during his Cubs tenure. Porter’s replacement, Zack Scott, was placed on administrative leave last month following his DWI arrest in White Plains. Scott pled not guilty and is awaiting a court hearing.

— Additional reporting by Joel Sherman