Charles Fernandez, who was also a director, stepped down on October 17 for what Fairholme chief Bruce Berkowitz said were "personal reasons."
The changes come after a rocky year for Berkowitz's flagship Fairholme Fund <FAIRX.O>, which has lost 26 percent of its net asset value this year through October 21.
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The performance is due to bets that have backfired on the insurer American International Group Inc <AIG.N>, Bank of America Corp <BAC.N> and Florida-based landowner and developer St Joe Co <JOE.N>. AIG, Fairholme's largest stock holding, is down 50 percent so far this year, while Bank of America has declined 52 percent and St Joe is off 32 percent.
In a statement, Berkowitz said Fairholme will "continue to stay the course" on its financial-stock investments.
Fernandez also resigned from his position as a board member of St Joe, according to a regulatory filing. Fairholme is the biggest shareholder of the company.
(Reporting by Lauren Tara LaCapra in New York, editing by Maureen Bavdek)