During the Mexican–American War, Houghton enlisted in the 1st Regiment of New York Volunteers, in June 1846. He arrived in San Francisco, California in 1847 with the rest of his regiment after sailing around Cape Horn. The regiment garrisoned Santa Barbara, before capturing the city of La Paz in Baja California. He was honorably discharged as a lieutenant at Monterey, California, in October 1848.
