William's admission was made to a fellow parent after he had earlier dropped off the four-year-old future king.
During a visit to Milton Keynes to celebrate the new town's 50th anniversary, he told mother-of-two Louise Smith, 31, about George's reluctance.
She said: "It was really exciting meeting William.
"He told me he'd just dropped Prince George off at school and he didn't want to go.
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"Sounds a bit like mine, really."
William had stopped to say hello to the mother and her daughters Sophia, aged three, and one-year-old Holly, as he toured a festival, staged in a park, showcasing the best of Milton Keynes.
After George's first day at Thomas's Battersea in September, William revealed the new starters had all taken the anxious moment in their stride while it was the parents who were full of nerves.
But at the time he reportedly hinted it might not always be plain sailing, saying: "We are all seeing how long that lasts before he doesn't want to go."