Paine was born in New Bedford, Massachusetts, the son of Vermont farmer Samuel Estabrook Paine and Massachusetts shopkeeper Mercy Coval Kirby Paine, and was moved to Bentonsport, Iowa when he was one year old. From early childhood until early adulthood, Paine lived in the village of Xenia in southern Illinois; here he received his schooling. His home in Xenia is still standing.
Paine's birthplace was New Bedford, Massachusetts, where he was born to Vermont farmer Samuel Estabrook Paine and Massachusetts shopkeeper Mercy Coval Kirby Paine. At one year old, the family moved to Bentonsport, Iowa.  He spent his early life in Xenia, Illinois, receiving his education there. His home in Xenia still stands today.