Pakistan Navy War College has progressed through the years. In nascent days, it began as small set up, Pakistan Navy Staff School established at PNS Himalaya, Karachi in 1968. The School aimed at conducting junior level Staff Courses. Only elementary staff work was taught to the officers. In 1970, the School was shifted to PNS Karsaz, Karachi. Efforts to upgrade the School to the level of Staff College commenced soon afterwards. On 6 May 1971, PN Staff College was formally inaugurated with the commencement of the first PN Staff Course.

By 1995 the requirement of Staff Course qualified officers in Pakistan Navy had increased manifold. The need to shift to a proper purpose built arrangement became inescapable. It was accordingly decided to move the College to Lahore. This decision was taken with a view to expand maritime culture in the country's heartland and to enlarge Pakistan Navy's outreach.

A building on the Mall Road (Shara-i-Quaid-e-Azam), Lahore was temporarily acquired from the Provincial government and speedily modified to accommodate the College. In August 1996, the building was inaugurated as Pakistan Navy War College. 25th PN Staff Course concurrently commenced at Lahore. It was nonetheless only a provisional arrangement. The foundation stone for a permanent building was laid at Naval Complex Walton, Lahore on 4 April 2011 by the then Chief of the Naval Staff. On 17 October 2014, the imposing grand structure that now houses the College was formally inaugurated by the Prime Minister of Pakistan.