Grehan initially featured as a trialist at the end of the 2021/22 campaign before making a permanent move to south London in the summer of 2022.
He was a key component of the Under-21s side last season, making 36 appearances in all competitions and helping the side to the final of the Premier League International Cup and a fourth place finish in the Premier League 2.
The centre-back has made 17 appearances in all competitions so far this season and also notched two goals.
Upon putting pen to paper on his new deal, Grehan said: “I’m delighted, over the moon. I’ve loved it here ever since I came over. I’ve been really enjoying my football, and I’m happy to be here for the next three years.”
Academy Director Gary Issott added: “Seán made a strong impression during his first season at the club and his hard work and determination has been rewarded with a new contract.
“He has not only slotted in well on the pitch, but also to life in south London, and I am sure he will continue to press on in the latter half of this season as he furthers his development.”