His career in the Navy progressed well and was the Flag Officer Sea Training of Pakistan Navy from 1980–84 as rear-admiral. In 1984, Vice-Admiral Khan was appointed as Commander of Pakistan Fleet and eventually appointed as Vice Chief of Naval Staff under Admiral Yastur-ul-Haq Malik, the Chief of Naval Staff. As VCNS, Vice-Admiral Khan was responsible for the naval warfare exercise and command structure of the Navy. After the death and state funeral of President Zia-ul-Haq, Vice-Admiral Khan supported then-Chief of Army Staff General Mirza Aslam Beg's decision for holding the general elections that saw the electoral victory of Benazir Bhutto and the Pakistan Peoples Party to form the government. Vice-Admiral Khan was later appointed as chairman of Pakistan National Shipping Corporation which he led from 11 November 1988 until 13 December 1990. Vice-Admiral Khan was promoted to four-star rank on 11 August 1991 by Prime Minister Benazir Bhutto. However, he was elevated as the Chief of Naval Staff when Admiral Malik left the command to him on 8 November 1991. It was during his stint as naval chief when the Pressler amendment came in effect that ultimately led to the military embargo on Pakistan and Navy lost eight of his surface ships that were to be returned to the United States in the 1990s. However, he successfully negotiated with Royal Navy's First Sea LordJulian Oswald who helped him closed a deal with the British government to sell the fleet of Type 21 frigates to Pakistan. This eventually resulted in commissioning the s in the 1990s. In an interview with Times Now an Urdu-language political correspondent, he ultimately warned of Indian Navy's expansion into the blue-water navy in order to establish the "Greater India." In 1994, Admiral Khan is said to have recommended against acquiring the designs and development of the Agosta 90Bravo-class submarines in coordination with France over the British Upholder-class submarine. His recommendations were bypassed by the government and the Agosta 90B-class submarines were acquired and built in successive long years.
Ambassadorship and retirement
On 9 November 1994, Admiral Saeed handed over the command to Admiral Mansurul Haq who was tenuring as the chairman of PNSC who was appointed by the Prime Minister Benazir Bhutto. After retirement from his military service, Admiral Saeed Khan was appointed as the Pakistan Ambassador to the Netherlands where he tenured for four years before returning to Pakistan.