John Edwin Holmes (December 28, 1809 – May 8, 1863) was an American lawyer, minister, and politician.

He was the 1st Lieutenant Governor of Wisconsin and a Union Army officer in the American Civil War.

He was captured by Confederate forces during the Battle of Brentwood and died of disease.

He moved to Hamilton, in Madison County, and studied while working to support himself, and was able to teach in a common school.

Holmes served on the Council of the Wisconsin Territory—the upper house of the territorial legislature—representing Jefferson and Dodge Counties through the final years before statehood.