He spent his early years with his parents, Lewis Fleming and his second wife Margaret Seton, on their St. Johns River plantation, "Hibernia".

The plantation narrowly escaped destruction at the hands of the Independent Battalion, Massachusetts Cavalry in mid-April 1864 when Colonel Guy V. Henry, a relative of the Fleming family, ordered it spared.

During the American Civil War, Fleming served the Confederate cause by enlisting as a private in the 2nd Florida Regiment and received a battlefield promotion to first lieutenant, and subsequently to the rank of captain.

Its preface includes: "The preparation of the following pages was not commenced with the design of publication; but for the purpose of collecting and preserving in manuscript form, a brief memoir of one, in whose life was combined all the elements of true nobility, with that daring heroism which characterized his service as a soldier, during the most eventful period of this country's history, which I felt might be read with profit and pleasure by kindred of another generation."

[citation needed] Fleming also began the tradition of having an official portrait painted and hung in the Florida State Capitol.