In the Civil War, he was a colonel and organized the 4th New York Heavy Artillery.

He raised and trained this regiment from New York that was stationed in Washington DC to defend the capital during the Civil War.

Doubleday and his wife, Mary Augusta Ward, resided on Staten Island.

17-year-old Stephen also served in his father's regiment as a lieutenant and was injured during the war.

Thomas D. Doubleday died on May 11, 1864, in New York City, after he had been accidentally run over by horse-drawn coach.