Gera suffered ligament damage during the FA Cup clash with QPR at Loftus Road earlier this month.
The Hungary international sustained a similar setback last season, which caused him to miss the second half of the campaign.
Clarke said: "Zoltan has had his operation, it went very well and his rehab starts this week.
"We would expect him to be up and running in time for pre-season training."
Clarke also expects midfielder Youssouf Mulumbu to return from African Nations Cup duty with DR Congo in time to be included in the squad for Sunday's home clash with Tottenham.
Mulumbu is due to fly back in the next couple of days after his country failed to reach the knockout stages of the competition.
Clarke said: "We expect him back on Friday and he will be in contention for Sunday. He's just played the three times for his country so there are no problems there."
Premier League Top 6 Finish 12/13 Top 6 Finish: West Brom 66/1
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