Shattuck was born in Crown Point, Essex County in northern New York state. His mother was Betsy Mather, a descendant of Increase Mather who was the president of Harvard from 1685 to 1701. His father Weston Shattuck, a native of Massachusetts, was a farmer who died when Francis was 12. Francis earned a teaching certificate by age 18 and was a schoolteacher for four years. He then moved to a small town in Vermont and worked as a store clerk, until he heard of the discovery of gold in California. He and a friend, George Blake, by then also his brother-in-law, took off for California.