Neill was born in Philadelphia. After studying at the University of Pennsylvania for some time, he enrolled at Amherst College and graduated from Amherst in 1842, then studied theology at Andover. After ordination as a Presbyterian minister, he moved to St. Paul, Minnesota, in 1848 where he became pastor of the First Presbyterian church. He also worked as Superintendent of Public Instruction for the Territory in 1851–53, and as chancellor of the State university in 1858–61. He wrote a large number of historical books, mostly of the Colonial period. The most important are: