The 35-year-old is facing 12 weeks on the sidelines after damaging a ligament in his shoulder during the 1-0 Barclays Premier League win at Everton on September 18.
However, Hughton is confident Harper will be back to play a key role again.
He said: "Particularly with goalkeepers, I don't think the age aspect comes into it.
"What you perhaps lose a little bit in age, you gain in experience, as Steve showed last season when he was outstanding.
"We would expect Steve to come back firing and looking into get straight back into that spot."