Wilpon has been at least partial owner of the New York Mets since 1980. He bought a very minor stake in 1980 when Doubleday Publishing bought the team. In 1986, Wilpon and Nelson Doubleday bought the team from the publishing company. Wilpon and partners bought out Nelson Doubleday in 2002 to take sole ownership of the team. He reached an interest to sell his majority interest, co-owned with other members of his family and brother-in-law Saul Katz under the name "Sterling Partners", to hedge fund billionaire Steven Cohen on September 14, 2020, for $2.4 billion. Cohen was already a minority owner, and a previous deal to sell him the team had fallen through due to Wilpon's insistence that his group continue to run the team for another five years after the sale.
In 2009, his name came out on a list of major investors to have been caught out in financier Bernie Madoff's massive fraudulent investment scheme; it was estimated that the Wilpon family had invested close to $550 million with Madoff's company. As the entire structure was a Ponzi scheme, Wilpon stood to lose the whole amount; worse, other investors who had lost everything in the collapse, led by bankruptcy trustee Irving Picard, were suing him for $1 billion to try to recover part of their losses from the remaining value of the Mets, Wilpon's most valuable asset. The reasoning was that Wilpon could not have invested such a massive amount of money without being privy to the shenanigans Madoff was up to, and that the Mets were in fact one of the few investors to have made money from Madoff's scheme. For his part, Wilpon defended himself by stating that he was a real estate specialist, not a financial investment expert, and that he had fully trusted Madoff with his funds; in fact, he had made a payment of $1 million to him just days before the whole pyramid collapsed, proving that he had no inkling of what was going on.
Wilpon did acknowledge that the Mets used Madoff's services in certain of their financial dealings, such as the infamous buy-out of Bobby Bonilla's contract after the 1999 season, which provided the outfielder with a payout of $1.2 million a year for 25 years; that deal was structured because the Mets thought they could extract a higher rate of return from Madoff than what they were paying Bonilla in interest on the money due to him. In fact, Bonilla ended up winning that deal easily when interest rates collapsed later that decade, but in the immediate, the Mets managed to free some cash to acquire pitcher Mike Hampton and outfielder Derek Bell. As a result, the whole situation cast a pall over the future of the Mets' ownership, with speculation that Wilpon would be forced to settle with Picard by ceding part ownership of the team in an out-of-court settlement of the lawsuit. On March 19, 2012, Wilpon and minority owner Saul Katz agreed to pay $162 million into a trust fund for Madoff's victims in settlement of Picard's suit; $29 million of that sum was to come from Wilpon and Katz's personal fortunes. The agreement did give the Mets three years before having to make a first payment, a period that could allow outside investors to inject enough cash to prevent the deal from putting a stranglehold on the team's future finances.
In 2011, Wilpon told Sports Illustrated that the Mets were bleeding cash and were going to lose $70 million that season. On May 26th, he sold a minority stake in the team to investor David Einhorn for $200 million, securing himself some financial breathing room. However, he then announced on September 1st that the deal had fallen through, supposedly because Einhorn had wanted to make "extensive changes" to the initial agreement. Wilpon said he would seek other investment partners, a requirement that was made more urgent when the terms of the settlement of the Madoff-related suit were made public. That is when Cohen came on board as a minority owner, acquiring 8% of the team's shares for $20 million in 2012.
Wilpon was described as a hands-on owner, who follows the intricacies of on-field decisions. He was known to comment publicly on the performance of individual players such as David Wright, Jose Reyes and Carlos Beltran. In the 2010s, he became less involved in day-to-day operations of the team, as his son Jeff Wilpon, was the Mets' chief operating officer. However, he was always consulted on major decisions affecting the franchise.
- Anthony DiComo: "Sterling Partners, Cohen agree to Mets sale", mlb.com, September 14, 2020. 
- Jeffrey Toobin: "Madoff's Curveball: Will Fred Wilpon be forced to sell the Mets?", The New Yorker, May 30, 2011.