Stoddard was born at Homer, Cortland Co., New York. His parents were Prentice S. and Sarah (Osborn) Stoddard. Stoddard attended the University of Rochester, where he graduated cum laude. On 25 Jul 1870 Stoddard married Susan Eagleson Cooper; they had five children. Stoddard died in Madison, New Jersey.
Stoddard's father was a bookseller, and Stoddard worked in his bookshop while growing up. After graduation, Stoddard was employed in an "editorial position" in 1857 at the Daily Ledger (Chicago); by 1858 he had become editor and proprietor of the Central Illinois Gazette, in Champaign, Illinois.
Stoddard knew Lincoln, worked hard for his election, and received a government appointment. He first served as a clerk in the Interior Department. On July 15, 1861, he was appointed "Secretary to the President to sign land patents." After a brief period of service in the Army, Stoddard became Assistant private secretary to Lincoln and "one of three people doing all the White House clerical work during the early Lincoln administration." Preparation of a digest of newspaper articles was one of his original responsibilities; it was stopped because, according to Stoddard, "Mr. Lincoln never found time to spend an hour upon laborious condensations." He personally made the first copy of the draft Emancipation Proclamation in September 1862.
After two bouts with typhoid, Stoddard left his White House post in July 1864. On 24 Sept. 1864 he was appointed United States Marshal for Arkansas; however, in 1865 he resigned for health reasons. He moved to New York City and worked on Wall Street. He entered government service again from 1871–73, this time for the government of New York City. He was a clerk for the Department of Docks.
Stoddard also received nine patents for inventions.
- Dismissed (1878)
- The Heart of It (1880)
- Dab Kinzer (1881)
- Esau Hardery (1882)
- Saltillo Boys (1882)
- Talking Leaves (1882)
- Among the Lakes (1883)
- Wrecked? (1883)
- Life of Abraham Lincoln (1884)
- Two arrows - a story of red and white (1886)
- The Lives of the Presidents (10 vols. 1886-9)
- The Red Beauty (1889)
- Crowded Out o' Crofield (1890)
- Inside the White House in War Times (1890)
- The Red Mustang
- The White Cave (1893)
- The Table Talk of Lincoln (1894)
- On the Old Frontier (1895)
- Winter Fun (1895)
- The Windfall (1896)
- The Lost Gold of the Montezumas (1897)
- With the Black Prince (1898)
- Ulric the Jarl (1899)
- Ned, the Son of Webb (1900)
- The Noank's Log (1900)
- Ahead of the Army (1903)
- The National Cyclopaedia of American Biography (Vol.8). New York: James T. White and Company. 1953. p. 121.
- Dictionary of American Biography (Vol. IX–Part II). New York: Charles Scribner's Sons. p. 60.