John Markle was born in Hazleton, Pennsylvania, the son of an anthracite operator, inventor, and financier. He grew up in coal country and studied mining engineering at Lafayette College, from which he graduated in 1880. That same year he was called on to manage the family enterprises when his father became ill. He served successfully as director of George B. Markle and Company for nearly fifty years and was known throughout the coal industry for his extensive reclamation of mines inundated by the great flood of 1886.

Markle believed that an individual who has funds beyond those needed for living expenses becomes "a trustee for his fellow man and should so use those funds." When he and Mrs. Mary E. Robinson Markle moved to New York City in 1902, he devoted himself to philanthropy as well as to his business interests. In 1927 he established the John and Mary R. Markle Foundation--the first foundation to name both husband and wife in its title--with an initial endowment of $3 million. The terms of his will later increased this amount to about $16 million. The Foundation's assets are now approximately $180 million.