"As a result of recent management changes at Heinz, we have decided to transition our business to other suppliers over time," McDonald's said in a statement.
"We have spoken to Heinz and plan to work together to ensure a smooth and orderly transition," said McDonald's, which has more than 34,000 restaurants around the globe.
A spokesman for Heinz did not immediately respond to requests for comment.
The switch will be more apparent overseas than in the United States, since McDonald's only serves Heinz ketchup in two domestic markets - Pittsburgh and Minneapolis, the Pittsburgh Post-Gazette reported on Friday.
The move from McDonald's could benefit Heinz ketchup rivals Hunt's, owned by ConAgra Foods Inc, and Del Monte.
Warren Buffett's Berkshire Hathaway and an investment fund affiliated with 3G Capital bought Heinz for $28 billion in June and immediately named Hees CEO.
Burger King went public in June 2012, less than two years after it was taken private by 3G Capital Management LLC, which retains a stake in the fast-food chain.
(Reporting by Lisa Baertlein in Los Angeles; Editing by Leslie Adler)