The move came hours after the club's new President Fernando Martin jumped ship. Fernandez is a close ally of Martin, whose departure stems from a high-profile meeting at the club in which some members were understood to question his presidential eligibility. Martin was rushed to the presidency in late February, following the unexpected resignation of predecessor Florentino Perez. Martin has said he will participate in the club's upcoming presidential elections, scheduled to take place before the summer.
"Martin quit and Fernandez has followed him," the Real Madrid spokeswoman said, adding that Martin is expected to return to his previous duties as chief executive of his PR shop Ares Comunicacion Corporativa.
The club has not appointed someone to replace Fernandez, the spokeswoman said, adding that such a move could come after the presidential elections.
Fernandez was appointed comms director on April 10, replacing Antonio Garcia Ferreras, who left the sports team to join fledgling Spanish TV broadcaster La Sexta.
The management crisis at Real Madrid, which employs English soccer star David Beckham, comes at a time of lacklustre performance at the team, which is eclipsing its stellar image in Europe.
Prior to starting his own company, Fernandez worked for Martin's real-estate company Grupo Inmobiliario Martinsa.