Thomson died in Philadelphia on May 27, 1874 and is interred at The Woodlands Cemetery. A historic marker commemorates the location of his birth in his hometown of Springfield (Delaware County), Pennsylvania, and a street in the community is named for him. The city of Thomson in McDuffie County, Georgia, was named for him. Andrew Carnegie was a great admirer and named his main company the J. Edgar Thomson Steel Company; Carnegie also named the Edgar Thomson Steel Works in Braddock, Pennsylvania, after him.