The west London club were relegated after they drew 0-0 with Reading last weekend, but Fernandes has warned fans that any hopes they had of an immediate promotion could be fanciful.
He told BBC Sport: "It might take us two or three seasons.
"We may have to [play the long game]. And there are a couple of things that we're looking at. Do we invest in lots and lots of young players like Aston Villa?
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"But we'll get the infrastructure of the players right. We've got everything else right in terms of the brand, in terms of the exposure, the plans for the training ground, the stadium. We've just got to get that player infrastructure right."
In a statement released on the club's website earlier this week, Fernandes had been particularly critical of certain players at the club and how their attitudes were not acceptable throughout the course of the season.
In his statement, Fernandes said: "It's heartbreaking for me when we lose. I don't want to go out, I just want to stay at home.
"I haven't said it throughout the season because it wasn't right to be said, but it hurt me when I saw some of the players who didn't feel the way I felt.
"And in fact, in their case, it should be worse because this is their job, it's their life. It was probably the low point for me when I saw the reaction of some of the players."