Sunday's 0-0 draw with Reading relegated the R's to the Championship, but Fernandes has said that the Englishman will lead the team into the new campaign.
"I have had a positive meeting with Harry. I don't think there was any point where he was thinking of not being with us and continuing this project he has embarked upon with a third of the season through," Fernandes told the club's official website.
"Harry is a football man and he knows what he wants in terms of players. We had a good discussion today with Ruben (Emir Gnanalingam), Philip (Beard, CEO) and Mark (Donnelly, COO) on the kind of players we want next season.
"Harry will not be forced to sell any players he wants to keep. We had a very good discussion on this. Harry has been very pragmatic and the shareholders have been very pragmatic. There are some players that we really want to keep and we will do our best to keep them. I think we will."
"It was a good meeting because we are all very clear on the timelines, we're very clear on what to do. We may not get everything we want but I am comforted by the fact we have a plan."
QPR host Arsenal in the Premier League on Saturday.