The second son born to Laetitia Corbin (c. 1657-1706) and her husband Colonel Richard Lee II (1647–1715), at his father's "Paradise" plantation in Gloucester County.
After the Board of Trade assumed responsibility for colonial operations and separated operations for the Colony of Virginia (where his father served on the Governor's Council), Philip Lee moved to the Province of Maryland in about 1700, and six years later married his first wife, Sarah Brooke, daughter of a member of the Maryland Governor's Council (this and a later marriage discussed separately below).
By 1710 he was one of the seven Justices of the Peace who adjudicated and administered the county, a position he would hold for at least a decade, although rarely present at sessions after the courthouse was moved from Charlestown to Upper Marlboro, Maryland in 1821.
From 1725 until his death, Lee was a member of the Upper House (also called the colony's King's Council, similar to that on which his father and later brother sat in Virginia).
At the time of his death, Lee owned some 2,467 acres (9.98 km2) and his estate was valued at 4,240 pounds of current money, including 87 slaves, 2 servants, 185 oz.
Her will made her brother Thomas Brooke Jr. executor on behalf of her youngest son, Arthur Lee, who inherited land along Rock Creek (some of which is now in Washington, D.C.) that was given to her by her father.
Francis Lee's will specifically gives his widow three male and three female Negro slaves and certain land unless she converts to Catholicism or marries, and names their children as Leticie [sic], Elizabeth, Alice, Hancock, Corbin, John, George and Margaret.