He attended the West Nottingham Academy in Colora, Maryland, and studied with the Reverend Samuel Finley, afterwards president of the College of New Jersey (later Princeton).

Heitman's Historical Register of Colonial Officers reports a John Filson served as an Ensign in Montgomery's Pennsylvania Battalion of the Flying Camp and was taken prisoner at Fort Washington on 16 November 1776, during the Battle of New York.

Gilbert Imlay reprinted Filson's entire work, along with other material, in A Topographical Description of the Western Territory of North America (volume II, published in London and New York in 1793).

After spending several years in Kentucky teaching school, surveying, trying (unsuccessfully) to start a seminary, and becoming embroiled in numerous lawsuits and financial difficulties, he purchased from Mathias Denman a one third interest in an 800-acre (3.2 km2) tract at the junction of the Ohio and Licking rivers, the future site of Cincinnati, which he called Losantiville, a name formed by Filson from the Latin "os" (mouth), the Greek "anti" (opposite), and the French "ville" (city), from its position opposite the mouth of the Licking River.

After his disappearance his partners, Denman and Patterson, transferred his interest in the site of Cincinnati to Israel Ludlow, and his heirs never reaped any benefit from the subsequent increase in the value of the land.