Mitroglou made his debut in last weekend's 1-1 Barclays Premier League draw at West Brom, but will not participate when Jose Mourinho's side visit Craven Cottage.
Magath insists the Greece forward, a deadline-day signing bought to fill the void created by Dimitar Berbatov's departure, is not yet ready for the demands of English football.
"Kostas is a very dangerous striker, but in this league you have to be fit if you are to be ready to score," Magath said.
"Next weekend (against Cardiff on March 8) I'm convinced that he will be back in the squad."
Magath is hoping to capitalise on Chelsea's Champions League fatigue when Fulham attempt to climb off the foot of the table by defeating the Premier League leaders.
The Blues were held to 1-1 draw against Galatasaray in Istanbul on Wednesday night and Magath insists they will have been drained by the travel.
"When a team has played in the Champions League, it is always an advantage," Magath said.
"We are lucky that Chelsea have had such a long trip to Istanbul to play on Wednesday
It's a good situation for us.
"I remember the situation - you have to stay at the airport, fly for a few hours and then play the game at night.
"Players can't sleep so well and are tired and then they have to spend more time at the airport
It bothers the players a lot.
"It gives us a chance
Chelsea are favourites, everyone knows that, but we'll try to fight and make a fast game.
"If we pressurise Chelsea then we have a good chance to win the game."
Fernando Amorebieta and Damien Duff are in the Whites' treatment room, but Darren Bent returns after missing the West Brom match for personal reasons.
Chelsea manager Mourinho will assess the fatigue levels of his squad following their midweek Champions League trip to Istanbul
David Luiz (groin) and John Obi Mikel (calf) are among those being checked, as are midfielder Oscar (ankle) and striker Fernando Torres.
Nemanja Matic and Mohamed Salah were cup-tied in Europe so should feature, but midfielder Marco van Ginkel is continuing his rehabilitation from his serious knee injury.
Mourinho has backed the claims of midfielder Frank Lampard that the Barclays Premier League has to do more to help clubs in Europe with fixture schedules.
The Blues have little recovery time following their midweek Champions League trip to Istanbul, having arrived back in the early hours of Thursday morning, before heading into the west London derby with Fulham at Craven Cottage on Saturday afternoon.
Mourinho's squad trained at Stamford Bridge on Thursday afternoon before the players headed off to their usual pre-match hotel at Chelsea Harbour.
Clubs who play in the Europa League on Thursday evenings are allowed to push their next domestic matches back to a Sunday kick-off, but there is no such dispensation for Champions League fixtures.
The Portuguese manager, whose side are top of the Premier League, insists Lampard was right to speak out against what he sees as poor planning, with little consideration for fatigue on players.
"We all prefer to play game after game after game, but we all want to play game after game with conditions to recover, with equal conditions for every team, and no sense that a team has a privilege in the choices, and every team in the same country has the same privilege to be a little bit protected in relation to European matches," said Mourinho, who will assess the fatigue levels of his squad before making a final team selection.
"It makes the players' job difficult, not my job.
"I can play a match every day, it is not a problem for me or the people who make the fixtures
I don't run, they don't run
It's difficult for the players.
"When a player like Frank Lampard, who has a right to speak and has played an unbelievable number of seasons and matches in this club, and over 100 times for England, and is not the kind of player who is trying to give an opinion all the time, so when a player like him, and a man like him, expresses his feelings about that, this country should listen."
Source : PA
Source: PA