Windsor, Slough, Eton and Hounslow Athletics Club normally use the park's famous Long Walk for winter training.
The Crown Estate now said the park's ground conditions are not suitable for the club's training sessions.
Coach John Higgins said: "Mo Farah used to train with the club, and he used to train exactly on this venue".
"It's really sad."
Mr Higgins said although the club used an athletics track for summer training, in winter it needed an outdoor venue for athletes to train on grass for cross country fixtures.
The club is used by children aged between eight to 18-years-old to train, and has been running since the 1880s, with Prince Philip as its current patron.
"We need somewhere lit and that's why the Long Walk is so perfect".
"It's a lovely place and we're very very careful about not littering, because we respect the place," he said.
Russell Young, a father of two children at the club, said: "We're extremely disappointed, we don't really cut up the grass.
"We thought they'd be quite happy to have children exercising on it."
The nearby playing fields of Eton, where the Thames Valley Athletics Centre is based, are not lit and have cricket pitches which could be damaged by runners, while Upton Park in Slough is not safe for the club to use at present as the pedestrian crossing is out of service following a collision with a lorry.
A spokesperson for Windsor Great Park said discussions were continuing with the club to find what other options may be available for the next season.
Young runners at Olympian Mo Farah's former athletics club have been banned from training at Windsor Great Park in preparation for cross country races.