The 21-year-old headed into the final day of action in Zagreb sat behind Frenchman Florent Amodio after the short program.
But all that changed when he got back out on the ice, finishing with 274.87 points, almost 24 points clear of his nearest challenger Amodio, who had to settle for silver after losing his lead to the Spaniard.
Amodio now has the full set in medals from the European Championships, his silver being added to a gold won in 2011 and a bronze he took home last year, while Fernandez's blew his previous best finish of sixth from 2012 out of the water.
And completing the podium in Croatia was Czech skater Michal Brezina as he took home bronze with 243.52 points.
