The Potters were pushed to the limit in their fourth-round tie against a Birmingham side who, despite seeing Wade Elliott sent off at the end of the first half, scored twice late on in normal time and then again at the end of extra time to force an incredible 4-4 draw at St Andrew's.
Stoke eventually triumphed 4-2 on penalties to make the last eight of the competition for only the third time since winning the League Cup back in 1972, the sole major honour in the club's 150-year history.
And Hughes, who won the trophy with three different clubs as a player but has only ever reached the semi-finals as a manager, would love to take the Staffordshire club to Wembley in his first season at the helm.
"We wanted to be in the next round and we've achieved that but we didn't think we'd have to go through the amount of emotion we've expended," he said.
"It should have a been a lot more comprehensive and comfortable for us. But we got through so we're grateful for that."
Hughes added: "You saw by my selection that it was a strong team and a team that was more than capable of winning the game and we got in a position where we should have won the game. It's just that last period that's disappointed us but we'll learn from that.
"Our fans here were magnificent and came out in numbers on a Tuesday night. They were great for us and it would be great to reward them for their support this year."
Sky Bet Championship side Birmingham, who won the competition in 2011, could arguably take more positives out of the tie despite their exit.
And proud Blues boss Lee Clark was clear in his praise for his side.
"They've given everything, they've ticked every box - pride, passion, work ethic, quality on the ball and never giving in," he said.
"I couldn't have wished or hoped for anything more than what those players have given me under those circumstances.
"I just wish Lady Luck would shine on us a little bit more than (she) has over the course of the season because there've been league games where we've deserved more than we've got."