The club's board of directors met after Deportivo drew 1-1 at home with La Liga's bottom club, Cordoba - their eighth straight match without a win.
The result left the Galician club just two points clear of the relegation zone with eight games left.
Deportivo's decision brought Fernandez's stint in charge to an end almost exactly nine months after he was appointed on July 10, 2014.
"Deportivo La Coruna want to sincerely thank Victor Fernandez," read a statement from the club.
"Your stake has been important in the return to La Liga, commitment to the White and Blues project and the work done since coming to the club until today.
"When the moment comes that a new coach has been hired, Deportivo's president will appear before the media for a presentation."
Deportivo needed an 87th-minute own goal from Cordoba's Florin Andone to claim a point on Wednesday, after the same player had given the visitors the lead nine minutes into the second half.
