The state of Missouri took possession of the Pacific Railroad in February 1866, when the company defaulted in its interest payment. In June 1866 the state conveyed the company to Fremont in a private sale. He reorganized its assets as the Southwest Pacific Railroad in August, but less than a year later (June 1867), the railroad was repossessed by the state after Fremont was unable to pay the second installment of the purchase price. The Panic of 1873, caused by over speculation in the railroad industry, and the depression that followed, wiped out much of Fremont's remaining wealth. Their financial straits required the Fremonts to sell Pocaho in 1875, and to move back to New York City.  Fremont was appointed Governor of the Arizona Territory by President Rutherford B. Hayes and served from 1878 to 1881. He spent little time in Arizona, and was asked to resume his duties in person or resign; Fremont chose resignation. Destitute, the family depended on the publication earnings of his wife Jessie.  Fremont lived on Staten Island in retirement. In April 1890, he was reappointed as a major general and then added to the Army's retired list, an action taken to ease his financial condition by enabling him to qualify for a pension.  On Sunday, July 13, 1890, Fremont (age 77) died of peritonitis at his residence at 49 West Twenty-fifth Street in New York. His death was unexpected and his brief illness was not generally known. On Tuesday, July 8, Fremont had been affected by the heat of a particularly hot summer day. On Wednesday he came down with a chill and was confined to his bedroom. His symptoms progressed to peritonitis (an abdominal infection) which caused his death. At the time he died, Fremont was popularly known as the "Pathfinder of the Rocky Mountains". He was buried in Rockland Cemetery in Sparkill, New York.

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