Manchester United have reached an initial agreement with Barca over the signing of the Spain international , with a total fee of €32 million - surpassing his €30m release clause - to be paid, depending on bonuses.
However, Fernandez remains upbeat that both Pedro and full-back Adriano will ultimately decide to remain at Camp Nou.
"Pedro's buyout clause is €30m. He is a player who has performed fantastically for Barca," Fernandez told reporters at his official presentation.
"Both the coach and I want him to stay. We don't want to lose him but we know that this is a risky situation and we will have to wait. If he goes, we will lose a lot of things.
"Adriano is a similar case to Pedro. We want him to stay and we think he will stay. The coach also considers him to be an important player.
"I spoke to them in San Francisco and I get the feeling that they will stay. We are working on it.
"If they stay, there will be no more signings, although we are always open to possibilities and always working for the good of the team."
Fernandez also confirmed that Alen Halilovic will be loaned out for the coming season and admitted that Adama Traore could also quit the club due to a lack of first-team opportunities.
"Halilovic is sure to go on loan to another team. We have told the player that is Barca's intention," he said.
"We will look for a loan deal where he can continue to develop as a player and come back next year. He's a young player with a lot of quality.
"Adama is a magnificent player but due to certain circumstances he hasn't managed to find a place in the first team. He might leave."
Fernandez has stressed, however, that all forthcoming transfers will have to be agreed upon with head coach Luis Enrique.
"I really got to know him two or three days after Barca won the Champions League in Berlin," he said. "I got a very positive feeling about him.
"We found that we think along the same lines. A technical secretary needs to have a good relationship with the coach. One of the reasons I am here is because I get on so well with him. We would never sign a player unless we both agreed on it."
