Cisse was absent on Saturday after being rushed to hospital with an infected toe prior to the international break.
The 29-year-old spent a couple of days on an IV drip to get antibiotics into his system.
"Kalifa actually collapsed after the game against Sheffield Wednesday and was rushed to hospital. It's been a pretty nasty toe injury," McClaren told the Derby Telegraph.
Mali international midfielder Cisse, who has signed a short-term deal with the Rams until January, made his debut in the 3-0 home victory over the Owls earlier this month before the drama unfolded.
First-team coach Paul Simpson added: "We are hoping Cisse is over the worst of it now.
"He has had a really tough time but we're hoping he will be back in training this week and will give us a selection decision for the next game.
"He was ruled out for the Bournemouth game but, fortunately, we had a great replacement in John Eustace."
Eustace returned to the team following a one-match suspension for reaching five yellow cards.