Stark was the eleventh of twelve children born to Adin Stark and Eleanor Stillwell Stark of Shelby County, Kentucky. He grew up in Gosport, Indiana, and served in the Union Army during the U.S. Civil War, where he played the bugle. He married Sarah Ann Casey and raised a family, earning his living as a farmer, first in Indiana and then in Missouri near Maysville. Eventually he tired of farming and moved to Cameron, where he went into the new business of ice-cream making. After moving to Chillicothe, he supplemented his income by selling organs and pianos. In 1885 he settled in Sedalia and entered the music business full-time, opening an office at 516 Ohio Street and founding John Stark and Son with his 15-year old son William. He got into the publishing business after buying out J. W. Truxel, one of his competitors, who owned seven copyrights.
It was in Sedalia that Stark heard Scott Joplin play The Maple Leaf Rag, and on August 10, 1899, he bought the number for fifty dollars plus royalties of one cent per copy. This is said to be the first time in history that a composer had earned royalties. It proved a prosperous arrangement for both men. After an inital printing of 5,000 copies, a million were eventually sold, which enabled Stark to open an office in St. Louis, Missouri (and, in 1905, New York City) and Joplin to engage in composing for a living. Over the next two decades, Stark published and promoted the "classic" style rag pioneered by Joplin with a lineup that included Joseph Lamb, James Scott, Arthur Marshall, Paul Pratt, Artie Matthews, Robert Hampton, J. Russel Robinson, and Etilmon J. Stark (his son).
After his wife died in 1910, Stark closed his New York office and returned to St. Louis. By this time New York's Tin Pan Alley was dominating ragtime music sales. He continued to bring out new rags until 1922, well after ragtime had succumbed to jazz, which Stark despised. He died in St. Louis in 1927.