He was sent to Port Royal, South Carolina in March 1862 as part of a contingent of teachers & school administrators from the New England Freedmen's Aid Society, of which his father was vice-president.

His administration of the financial affairs of the college was noted to be remarkable for its skill and success "...in spite of adverse conditions and troublous times.

[6] After his retirement, Hooper devoted his time to the care of large trust properties and was one of the original trustees of the Boston Museum of Fine Arts.

His papers, dated from 1862 to 1866, relating to military service in South Carolina and New York during the Civil War are in the collection of the Houghton Library at Harvard University.

The papers primarily consist of financial reports, invoices, receipts, and other documents relating to Hooper's term of service.

Some letters are included in the collection; among them are three from Edward L. Pierce to Salmon P. Chase, Secretary of the Treasury, concerning the Port Royal Experiment.