After retirement, he joined the faculty of the Bahria University and penned columns on maritime security, Pakistan Today.

[4][6] In 1986, he attended the Naval War College in Rhode Island, United States, attaining his diploma in staff course.

[4] In 1992–95, Capt Humayun was selected by the Ministry of Defence (MoD) to serve as the naval attaché at the High Commission of Pakistan in New Delhi.

[4] The same year, Rear-Admiral Humayun participated in the Exercise Sea Spark, alongside then-Rear-Admiral Noman Bashir.

[6] In 2008, Vice-Admiral Humayun and Vice-Admiral Bashir were considered for promotion as four-star admiral in the Navy and being appointed as the Chief of Naval Staff, in a nomination summary sent by then-Defence Minister Ahmad Mukhtar to the Prime minister Yousaf Raza Gillani.

[5] Humayun served as the Vice Chief of Naval Staff until 26 December 2009 and retired from the Navy after completing his term.