Henry Van Rensselaer was born at the manor house in Albany, New York. He was the son of Stephen Van Rensselaer III (1764–1839), who was also a Representative and founder of the Rensselaer Polytechnic Institute and Cornelia Paterson, the daughter of William Paterson, the 2nd Governor of New Jersey, and later, an Associate Justice of the Supreme Court of the United States.
Henry was a student, and graduated from the United States Military Academy at West Point, New York in 1831.
He was appointed a brevet Second Lieutenant of the Fifth Regiment, United States Infantry on July 1, 1831, and resigned January 27, 1832. He then engaged in agricultural pursuits near Ogdensburg, New York, and served as a military aide to Governor William H. Seward from 1839 to 1840.
Upon his father's death in 1839, Van Rensselaer, as the fifth son, inherited the wild lands in St. Lawrence County along the St. Lawrence River. His eldest brother, Stephen Van Rensselaer IV inherited the manor on the Albany side of the Hudson River.
Van Rensselaer was elected as a Whig to the Twenty-seventh United States Congress, and served from March 4, 1841 to March 3, 1843. He was subsequently president of several mining companies, including the American Mineral Company and the Consolidated Franklinite Company. He was a director of the Northern Railroad (later the Rutland Railroad), but resigned to help found the Ogdensburg, Clayton and Rome Railroad.
Upon the outbreak of the American Civil War, he reentered the military service with the rank of colonel in the Union Army, and was appointed chief of staff to General Winfield Scott. From 1861 until his death, he served as an inspector general of several corps and departments including the 1st Army Corps, Department of the Rappahannock, 3rd Army Corps and Department of the Ohio.
On August 22, 1833, Van Rensselaer married Elizabeth Ray King (1815–1900), daughter of John Alsop King (1788–1867), the Governor of New York, and Mary Ray. Elizabeth's maternal grandfather was U.S. Senator Rufus King (1755–1827) and her great-grandfather was John Alsop (1724–1792), a prominent New York City merchant. Together, they had:Mary Van Rensselaer (1834–1902), who married John Henry Screven (1823–1903) in 1874
Cornelia Van Rensselaer (1836–1864), who married James Lenox Kennedy (d. 1864)
Stephen Van Rensselaer (1838–1904), who married Mathilda Coster Heckscher (1838–1915)
Henry Van Rensselaer, who died young
Euphemia Van Rensselaer (1842–), who became a Sister of Charity and took the name Marie Dolores.
Elizabeth Van Rensselaer (1845–1911), who married George Waddington (1840–1915), a son of William D. Waddington (1811–1886) and Mary Elizabeth Ogden (1810–1867).
John King Van Rensselaer (1847–1909), who married May Denning King (1848–1925), granddaughter of James Gore King.
Katherine Van Rensselaer (1849–1901), who married Dr. Francis Delafield (1841–1915), son of Dr. Edward Delafied, in 1870.
Henry Van Rensselaer (1851–1907), who joined the Society of Jesuits
Westerlo Van Rensselaer (1853–1857), who died young.
Van Rensselaer died of typhoid fever in Cincinnati, Ohio shortly before the end of the War. He was interred in the Grace Episcopal Churchyard, in Jamaica, Queens in New York City.
Through his son, John King Van Rensselaer, he was the grandfather of John Alexander Van Rensselaer (b. 1872), who married Helen F. Galindo in 1896, and who was arrested in 1908 for attempting to extort $5,000 from his mother.
Through his granddaughter, Julia Floyd Delafield, Henry was the great-grandparents of Floyd Crosby (1899–1985), the father of David Crosby and Jane Wyatt.