McGugan has not been named in the starting line-up or on the substitutes' bench for the Owls last two matches against Burnley and Bolton Wanderers, but Carvalhal insists that there is no problem.
To the contrary, he says that he has complete faith in the attacking midfielder and he hasn't ruled out bringing him back into the side which faces Fulham at the weekend.
"He's a player we believe in 100 per cent," Carvalhal said. "He has quality. At the moment the players we have in midfield have a good dynamic. They are attacking and defending well, and we are happy with them.
"This doesn't mean we are not happy with Lewis, or anyone else not in the team. After some time, we will be doing the opposite question - Lewis will be playing, and somebody else will be out. This doesn't mean that McGugan can't play in the next match, we trust in him."
McGugan was one of Wednesday's star players during a loan spell at Hillsborough last season, where he made 22 appearances and scored three goals.
He completed a permanent move from Watford this summer and was expected to play a similarly important role in the team, but he has found chances limited.
McGugan has not played for Wednesday since 19th August, and has been overlooked in favour of some of the other options Carvalhal has at his disposal.
However, with the Owls struggling to create chances, supporters have started to call for McGugan to come back into the starting line-up, and Carvalhal will be under pressure to ensure that he gets his selections right if he does continue to omit the 26-year-old from his team.