Neymar, who was linked with a move to Manchester United in the off-season, has been in talks over a fresh deal since the beginning of the campaign.
The Brazilian is currently committed to Barca until 2018.
"There will be an agreement with Neymar," Fernandez told TV3.
"I have no doubt about it – he will be at Barcelona for many years.
"When one starts with the intention to renew, we all know that we can reach an agreement.
"We are all in agreement that Neymar will stay here at Barcelona. The player has expressed it publicly, his camp too.
"Neymar is content and happy at Barcelona and that is the most important thing for us.
"We must face the situation calmly, thinking that if we have now finalised Rafinha's renewal, an agreement for Neymar's renewal will also be reached."
Neymar has netted 12 goals in 11 La Liga outings in 2015/16.