The Portuguese is already without Eric Bailly who has a back injury, while Luke Shaw and Antonio Valencia are nursing knocks and Ashley Young is suspended for the clash.
Smalling sustained a hairline fracture in his left foot during the Red Devils' narrow victory against Young Boys.
The 29-year-old was sidelined for United's 2-2 draw with Southampton on the weekend and Mourinho was forced to play a makeshift defence of Scott McTominay, Phil Jones and Nemanja Matic.
However Smalling is hoping he will be fit to return for the Arsenal game on Wednesday.
Jones is also facing a race against time to be fit for the match at Old Trafford after undergoing scans on a slight injury on the weekend.
And Mourinho is also waiting to see how Marcus Rashford, who asked to be brought off on Saturday, responds to treatment on an ankle injury.
In a rare bit of positive news for Man Utd, Marcos Rojo could make a return to play his first competitive match since the World Cup in June.
But the news will do little to change the mood of Mourinho's camp.
After the Saints draw, Mourinho reportedly called French ace Paul Pogba a "virus".
The former Chelsea chief apparently said: "You are like a person with a flu with a virus in a closed room – you pass that virus to the others."
This latest development is just one of a series of leaks from the club this term.
And there is no doubting the Red Devils are in a major crisis.
Following Mark Hughes' sacking Mourinho is now the favourite to be the next Premier League boss to be sacked.
Old Trafford top brass could call time on the Portuguese if his side succumb to another dismal result against the Gunners.
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