Stephanus van Cortlandt was born on May 7, 1643, the son of Captain Olof Stevense van Cortlandt. His father had been born at Wijk bij Duurstede, in the Dutch Republic, and in 1637 arrived in New Amsterdam. Beginning as a soldier and bookkeeper, Olof Stevense van Cortland rose to high office in the colonial service of the Dutch West India Company, serving many terms as burgomaster and alderman before dying in 1684. His mother was Anna ("Annetje") Loockermans van Cortlandt (born Turnhout March 17, 1618) who may have been the person who began the custom of Santa Claus in America.
His parents had four children: Stephanus van Cortlandt (1643 –1700); Jacobus van Cortlandt (1658–1739), who married Eva de Vries Philipse (born 1660); Maria van Cortlandt, who married Jeremias van Rensselaer (1632–1674); and Catherine van Cortlandt, who married firstly Johannes Derval and secondly, after his death, Frederick Philipse (1626–1702), the first lord of Philipsborough Manor. Philipse was previously married to Margaret Hardenbroeck (1637–1691) and during that marriage, had adopted her daughter, Eva de Vries (born 1660), who thus took the name of Philipse. Eva's father and Margaret's first husband was Peter Rudolphus de Vries (died 1661).
In 1668, he was appointed ensign of one of the militia companies of New York City. In 1677, he was appointed mayor of New York City, at the age of thirty-four, becoming the first mayor of New York City who had been born in America. He was reportedly appointed due to his intelligence, and social position in the community, as he was appointed by the English Governor. During his time in office, he remained an adherent of the aristocratic party, especially during the Leisler affair from 1689 to 1691. When Delanoy, the Leisler candidate, was elected to the mayoralty, in place of Van Cortland, the latter refused to deliver up the city seal. It has been said that when a committee came to his home, his wife shut the door in their faces.
Van Cortlandt married Gertruj van Schuyler (b. 4 February 1654), the daughter of Philip Pieterse Schuyler (1628–1683) and the sister of Pieter Schuyler, a colonial governor of New York and mayor of Albany. They lived at the "Waterside," on the present line of Pearl street, near Broad, where he engaged in business as a merchant. Together, they had:Margaretta van Cortlandt (1674–?), who married Judge Samuel Bayard (1669-?), the son of Nicholas Bayard (1644–1707) and descendant from the Stuyvesant family. A number of their descendants were Loyalists who relocated to England.
Anne van Cortlandt (1676–1724), who married Stephen DeLancey (1663–1741)
Catherine van Cortlandt, who married New Jersey politician Andrew Johnston (1694-1762), the son of John Johnstone (1661–1732), the 32nd Mayor of New York City.
Elizabeth van Cortlandt, who married the Reverend William Skinner
Philip van Cortlandt (1683–1746), who married Catherine de Peyster
His granddaughter, Gertrude Bayard, married Peter Kemble (1704–1789), a prominent New Jersey businessman and politician, and his great-granddaughter, Margaret Kemble (1734–1824), married Thomas Gage (1718/19–1787) who was General of the British Army during the American Revolutionary War. Descendants of this union are found in England, including amongst the Viscount Gages and the noble Bertie family in England (including those holding the title of Earls of Abingdon). A grandson, James DeLancey (1703–1760) became New York Governor, and granddaughter Susannah DeLancey (1707–1771) married Vice-Admiral Sir Peter Warren (1703–1752). Another grandson, Oliver De Lancey Sr. (1718–1785) married Phila Franks, daughter of a prominent New York Jewish family.
Grandson, Lt. General William Skinner, was an American Revolutionary Loyalist whose son, Brig. Gen. Cortlandt Skinner (1727–1799) was also a Loyalist who married Elizabeth Kearney (1731–1810). Another grandson, Pierre Van Cortlandt (1721–1814) was the 1st Lieutenant Governor of New York who married to Joanna Livingston (granddaughter of Robert Livingston). Their descendants include Philip Van Cortlandt (1749-1831) and Pierre Van Cortlandt, Jr. (1762–1848).