John E. Winn was born in December 1882 in Wisconsin to Colonel William M. Winn and an unknown mother.

He had two younger brothers, twins Milton Winn and Grover C. Winn, who were born in January 1886 in Wisconsin.

His father later married Anna Sarah Milbourn on December 10, 1892, in Woodford, Lafayette County, Wisconsin. The family moved to Juneau, Alaska, in 1893.

John’s half-brother, Burdette A. Winn, was born in Juneau on March 21, 1896.