Gates was born in West Chicago, Illinois (then known as Turner Junction) on May 18, 1855. He was the son of Asel A. and Mary Warne Gates. Gates had two older brothers, George and Gilbert, but both had died by the time he was 15 years old. While Gates was raised in a religious household, his mother, Mary, became more religious after the deaths of her two older sons. Because he had been involved in some harmless childhood mischief in both grammar and Sunday School, he was accused of stealing a collection at the Sunday School. He was barred from attending church as a result.