Clarke had made 14 appearances for Stoke and claimed two assists in the Championship after his loan move from Tottenham in January.
The 20-year-old was struck with bad news on Thursday after it was revealed to him that he will miss the rest of the 2020/21 season due to ligament damage in his ankle.
The injury sees Clarke return to the Tottenham Hotspur Stadium as O’Neill revealed his disappointment at the loss of the youngster before his loan spell expired.
O’Neill insisted that he could have done more with Clarke with eight games remaining for Stoke in the Championship, but stated that he was pleased with the young winger’s contributions.
“Jack hasn’t gone yet but he’ll go this week”, O’Neill was quoted as saying by football.london.
“Unfortunately he won’t play again this season, he has ligament damage in his ankle. He had a scan yesterday so that’s disappointing.
“We could have done with him.
“We could have done with more from him in the final eight games of the season.
“It’s never nice when a loan is cut short like that.
“He struggled a bit to start in recent weeks because the system made it difficult for him but overall we’ve been pleased with the contribution he’s made.”
Clarke will look to find a place in the Tottenham squad for next season after making two Europa League appearances and an FA Cup appearance for Spurs this season.