Harper was a pewholder at St. Stephen's Episcopal Church. He died in Philadelphia on March 31, 1873, and was interred in Laurel Hill Cemetery.
In Philadelphia Harper was a member of the Board of Guardians of the Poor and of the Board of Prison Inspectors. A patron of science, Harper was one of the founders of the Franklin Institute in 1824, and a delegate to the Great Exhibition of the Works of Industry of all Nations (often called the "Crystal Palace Exhibition") in London in 1851.