He served in the second war with India in 1965, and in third war with India in 1971 where he served on the destroyer as an executive officer. In 1973, Commander Khalil commanded the PNS Alamgir until 1976 when he was selected to assume the command of the Royal Bahrain Naval Force, which Captain Khalil commanded until 1988. In addition, he went to attend the Naval War College in Lahore.