The existing old building of the college was once used as Industrial Home. In 1993 Pakistan Navy Women Association donated this building to start as School to provide quality education to children of low paid employees of Pakistan Navy and other government servants residing in and around Naval Complex. Initially it was planned to be a primary School. However, with increasing strength of students the need was felt gradually upgrade it.
- In 1996, PN Model School was taken over by the Director Naval Educational Services and it got linked with chain of colleges run under Pakistan Navy Educational Trust (PNET). The Trust works under Naval Headquarters and runs 16 Schools at Karachi under the local administrative control of Commander Karachi. In 1997, the School was delinked from PNET and placed under Commander North.
- In 1999, Commander North appointed Principal Bahria College Islamabad as its Administrator to look after all its affairs.
- The institute was further upgraded to HSSC level in 2013 to offer education in Pre Engineering and Pre Medical disciplines and named as PN Model College Islamabad.
- In 2016, the college has been renamed as Bahria Model College Islamabad under a policy decision and started offering Science General Group (ICS).
- In 2020, the college has been renamed as Bahria College Zafar Campus Islamabad.