He attended local private schools, then Rensselaer Polytechnic Institute in New York City, from which he received a civil engineering degree in 1862.

After graduation, although his father was a Unionist, John Underwood enlisted in the Confederate States Army Engineer Corps, serving in Virginia and Tennessee.

He raised money to construct a Confederate Memorial at Oak Woods Cemetery in Chicago, Illinois to commemorate the Confederate prisoners who died at Camp Douglas, and whose remains were exhumed and moved there after closure of the previous cemetery and expansion of Grant Park during urban renewal following the Great Chicago Fire of 1871.

In 1910, oil portraits of many of the twenty Confederate generals he had commissioned from E.F. Andrews were auctioned by a Covington, Kentucky warehouse to pay storage fees, and most ended up in Virginia.

Western Kentucky University has several of his commissioned paintings and maintains some of his papers (as well as those of his Unionist father and paternal uncle), including letters available online.