John Stoughton Newberry was born on November 18, 1826 in Sangerfield, New York, United States. He was the son of Elihu and Rhoda (Phelps) Newberry. He was a descendant of Thomas Newberry who emigrated from Devonshire, England, to Dorchester, Massachussets, in 1634. Oliver and Walter Loomis Newberry were John's uncles. Elihu moved from Oneida County westward, finally settling at Romeo, Michigan.