In 1988, Harper joined the Australian Army in which he served for eight years before transferring to the New Zealand Army. He earned a Doctor of Philosophy in 2001 from the University of New England with a thesis on Howard Kippenberger, a New Zealand general of the Second World War. Harper was the official historian for New Zealand's military deployment to East Timor from 1999 to 2001. He retired from the New Zealand Army in 2001 with the rank of lieutenant colonel. He became a lecturer at Massey University in Palmerston North, and was made an associate professor in military studies the following year. In 2003 he was appointed director of the Centre for Defence Studies. He is currently Professor of War Studies at Massey University, and supervises doctoral students.