Despite his contract expiring in mid-2018, Iniesta is yet to renew at Barca, where he came through the famed La Masia academy.
Iniesta, 32, has won eight LaLiga titles and four Champions Leagues among numerous other trophies at the club.
While the Spanish World Cup and European Championship winner is yet to re-sign, Fernandez believes Iniesta will stay at Barca.
"We want Iniesta to continue with us for many years to come," he told Movistar.
"I hope he will be with us for a long time. I have no doubt that he will.
"I have no doubt that it will be so."
Iniesta played a full game as Barca recorded a 4-2 win over Valencia in La Liga on Sunday.