Pogba has not played since suffering a hamstring injury in the first half of a 3-0 Champions League win over Basel on September 12, while Fellaini has been out since picking up a knee injury during the international break.
With club captain Michael Carrick also unavailable, United's midfield depth has been tested, with Nemanja Matic and Ander Herrera playing in both the 0-0 draw with Liverpool last weekend and the 1-0 win over Benfica on Wednesday.
Mourinho is hopeful he could have more players available for the Premier League trip to Kirklees Stadium, but says there are no guarantees.
"Hopefully some of them [can return at Huddersfield] but I don't know. I don't know about Paul, I don't know about Fellaini," he said.
Centre-back Phil Jones was another to sit out the 1-0 win at Estadio da Luz but Mourinho is confident he will return on Saturday, with Eric Bailly unlikely to be ready.
"Phil Jones was on the bench because he felt that if we really needed him, he could [play]," said Mourinho.
"So if he was at that stage, on Saturday I think he will be in a condition to play. For Eric Bailly, I think it will be difficult."