James Macfarlane was born on September 2, 1819, in Gettysburg, Adams, Pennsylvania.

He was an American civil engineer, lawyer, geologist, and author. He studied civil engineering at Pennsylvania College and in 1837, he joined the corps of civil engineers of the North Branch canal, with headquarters at Towanda. In 1845, he was admitted to the bar and practised law, serving three years as District Attorney in New Bloomfield, Perry County. In 1851, he returned to Bradford County to practice law at Towanda and was elected its District Attorney (1852-1859). He served as General Superintendent of the Barclay Coal Company (1859-1865) and then became General Sales Agent of the Associated Blossburg Coal Company at Rochester, Syracuse, and Elmira, New York. In 1872, Pennsylvania College conferred upon him the degree of Doctor of Philosophy. In 1874, he was appointed one of ten Commissioners for the Second Geological Survey. He became a member of the American Association for the Advancement of Science in 1880 and fellow in 1882. In 1883, he was elected a member of the American Philosophical Society. He wrote "The Coal Regions of America, Their Topography, Geology and Development" (1873), regarded by scientists everywhere as the standard work on the subject. He was also the author of "Geologists' Traveling Hand Book: an American Geological Railway Guide" (1879). He contributed numerous geological articles to the American Encyclopedia and was a frequent contributor to well-known scientific periodicals Science and American Geologist.

In 1847, he married Mary Eliza Overton (1823–1888). He died on October 12, 1885, in Towanda, Bradford, Pennsylvania.