"The 10-year McDonald's/Disney alliance is ending for sound business reasons on both sides," said McDonald’s senior vice president for corporate relations, Jack Daly.
"This was a mutual decision made more than a year ago, a fact that is well known in the business world," he said.
Mr Daly rejected a Los Angeles Times story that said Disney was abandoning the pact because it does not want to be linked to junk food. The report was "based on Hollywood hearsay" and was "a misrepresentation of the truth", he said.
The marketing alliance between two of the most iconic US brands will end with this summer's release of the Pixar movies "Cars" and Disney's "Pirates of the Caribbean: Dead Man's Chest".
Its conclusion comes after McDonald's, in July last year, ended an exclusive tie-up with Disney and signed a two-year worldwide marketing deal with DreamWorks Animation.
The arrangement starts next year and will see McDonald's snatch the Oscar-winning green ogre Shrek among other DreamWorks characters from rival chain Burger King.
Deal vindicated
But at the time, McDonald's said it was negotiating a possible extension of its partnership with Disney, including the placement of McDonald's restaurants at Disney theme parks.
Mr Daly said the DreamWorks deal was vindication of the decision by McDonald's to go for "more flexibility and options in our entertainment relationships".
For a decade, McDonald's has tied its products in with new Disney releases through an array of marketing promotions including movie-character figurines in its children's Happy Meals.
For Disney, the deal was worth royalties of US$100 million (A$130.29 million) a year, the LA Times reported.
But the newspaper said that Disney executives had grown more concerned about linking cartoon characters to the fattening fast food that is most associated with McDonald's.
Apple Computer boss Steve Jobs, who joined Disney's board after the conclusion last week of the company's acquisition of his Pixar Animation Studios, has voiced concerns over childhood obesity in the past.
The issue has been rising up the political agenda in the United States, home to the highest rates of obesity in the world.
Nine million US children are overweight and 70 percent risk becoming as overweight or obese as adults.