John Alsop Paine was born on January 14, 1840, in Newark, New Jersey.

He was a Presbyterian minister, botanist, educator, archaeologist, and editor. He graduated from Hamilton College (B.A., 1859) and Andover Theological Seminary (M.Div., 1862). After working as a botanist at the University of the State of New York (1862-1865), he continued his studies at the Sheffield Scientific School of Yale University and the Columbia School of Mines (1865-1866). In 1867, he was ordained a Presbyterian minister and from 1867 to 1869, he was a professor of natural science at the Christian missionary institution Robert College in Istanbul. From 1869 to 1870, he studied at the University of Halle and Leipzig. He taught natural history and German at Lake Forest University in Illinois (1870-1871). Paine was an associate editor for The Independent (1871-1872). From 1872 to 1874, he was an archaeologist and naturalist with the American Palestine Exploration Society working in Syria, east of the Jordan River and the Dead Sea. In 1874, he received an honorary doctorate from Hamilton College in recognition of his research in Palestine. He edited the Journal of Christian Philosophy in New York (1882-1884) and he was on the editorial staff for the Century Dictionary in 1888. Paine was also Curator of Casts with the Metropolitan Museum of Art in New York City (1889-1906). He published several papers in the Journal of the American Oriental Society.

About 1864 he married Maggie (1840-1876), and in 1877, he married Emma Sophia Gillett (1842–1919). He died on July 24, 1912, in Tarrytown, New York.