The couple, which purchased the club for $430 million in 2004 from News Corp., married in 1979 and has four sons.
"Frank McCourt and Jamie McCourt confirm that they are separated," the club said in a release. "This is a personal matter and they request that their privacy be respected. They will be making no public statements."
The team has reached the postseason in four of the six years the McCourts have owned the club and opens the NL Championship Series against the Phillies at home Thursday.
Frank McCourt is a Boston native who founded The McCourt Company, which develops commercial real estate projects. The company was moved from Boston to Los Angeles in 2006 and is now called The McCourt Group. The president of that company is the McCourts' son Drew.
Jamie McCourt is a Baltimore native who was named vice chairman when the club was transferred from News Corp., then president in 2005 and CEO earlier this year when Dennis Mannion was promoted to club president and chief operating officer.
Ken Gurnick is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.