In 1859, the British Royal Navy in India established its first command post in Manora Fort when Captain Thomas Maitland from HMS Wellesley succeeded in capturing most of the southern region of British India, which now is modern-day Pakistan.

: 473 [1] In 1864, the Gen. Charles James Napier had built city's one of first Church and the first Lighthouse in 1888.: 475 [1] On 14 August 1947, Vice Admiral James Wilfred decided to move the command post from Monora Island to Mules Mansion in Karachi– nation's first capital.

[2]: 126 [3] Based in Mules Mansion in Karachi, the Navy's NHQ faced many problems relating to strategic communication with the Air Force HQ (in Peshawar at that time) and the Army GHQ (then in Rawalpindi), operational planning, and execution that resulted in military's overall performance failure in 1971.: 69 [4] Recommendations accepted from the report of the War Enquiry Commission, the Navy's NHQ was shifted Islamabad to provide coordination with the Army's GHQ on 15 March 1975.: 69 [4] Initially, Navy's NHQ was housed in a government secretariat building Islamabad but later built its own headquarter buildings in Islamabad.

: 86–87 [6] There are three chief of staff branches that composed of multiple offices to oversee the administrative operations of the navy.

[7] In fact, the Navy's NHQ functions exactly on similar protocol of Army GHQ.