The English Championship finishes on May 2 and the FA Cup final is on May 30 so with Reading unable to make the promotion playoffs, they would have nearly a month to prepare.
Clarke is frustrated his players could be left twiddling their thumbs if they knock Arsenal out.
"When we beat Arsenal, we have to wait four weeks after our last league game to play the Cup final," Clarke told reporters.
"There wasn't a slip of the tongue there. Four weeks? I'll probably need to go on holiday for two of those and then bring the team back in. It's a long break.
"If we get to the final, what are we going to do from May 2 to May 30? What do we do? Everyone else has played, so we won't be playing games.
"It would be a great puzzle to have though. Let's talk about it on Saturday night."
Reading, who have dropped to 18th in the Championship and are without a win in their last five league matches, reached an FA Cup semi-final for the first time in 88 years after beating League One side Bradford City in a quarter-final replay.
Holders Arsenal, winners of 16 of their last 18 matches in all competitions and who have never lost to Reading, are massive favourites to reach the final.
Clarke, who won the FA Cup as a player and a coach with Chelsea, said he does not get "too carried away with the favourite and underdog tags" but is hoping the in-form Gunners have an off day at Wembley.
"I've had lots of experiences at Wembley," Clarke told Jack FM. "Semis are all about winning. It's not a game you like to lose because the losers of semi-finals get forgotten about.
"Saturday is a game of football -- 11 v 11. On the day, we have to hope that Arsenal are not at their best because if they are then it will be very difficult for us.
"If Arsenal are a bit below their best, and we play as well as we can then, in football, you never know."
(Reporting By Michael Hann; editing by Martyn Herman)
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