Paul Nicholls said his staff had put in a "massive effort" overnight to rescue 15 animals.
Mr Nicholls, who trained National Hunt chaser See More Business and record-breaker Kauto Star, said water poured into the yard at Ditcheat, Somerset, reaching a depth of about 3ft.
A clear-up operation is ongoing at the yard following the flood.
Mr Nicholls said the water has now gone and the horses are being returned to their stables.
Racehorses at a champion trainer's yard had to be rescued after flash floods hit their stables.