John McClintock, Jr., was born in Philadelphia, Pennsylvania, on October 27, 1814, the son of Scottish immigrants John McClintock (1784-1856) and Martha McMackin (d. 1840). He had 7 siblings: James (1809-1881), Jane (1811-1884), William (b. 1817), Robert (1819-1889), Martha (1821-1900), Samuel (b. 1826), and Margaret (1828-1856). McClintock moved to New York City in 1830, where he worked as a bookkeeper at the Methodist Book Concern. In 1832, he began studies at the University of Pennsylvania; he graduated in 1835 and became a Methodist pastor in Jersey City, New Jersey. In 1836, he moved to Carlisle, Pennsylvania, where he became a professor of mathematics, and later of classical languages, at Dickinson College. He left the college in 1848, when he became editor of the Methodist Quarterly Review, a position he held until 1856. During his time as editor, McClintock worked to facilitate philosophical debate among American positivists, and to advocate against slavery. From 1857-1860, he was minister of St. Paul's Methodist Church in New York City, and from 1860-1864 he was a pastor for the American Chapel in Paris, France, where he promoted the Union cause to his European audience during the Civil War.
McClintock served as the first president of the Drew Theological Seminary (later Drew University) in Madison, New Jersey, from 1867 until his death in 1870. McClintock married Caroline Augusta Wakeman in 1836; they had two surviving children: [John?] Emory (1840-1916) and Augusta (1843-1928). After his wife's death in 1850, McClintock married Catherine Wilkins Stevenson Emory (1819-1891); they had one surviving daughter, Anne (b. 1859). John McClintock, Jr., died on March 4, 1870.