Prior to partition, the present Benazir Bhutto International Airport was known as “Chaklala Airbase”. The air strip and a hanger portion of the aerodrome were built in the year 1930s. It served as standby strip for the British Air force during the World War II.

In 1948, Pak Airways and Orient Airways commenced their operation with DC-3 and conveyor (DCA) type of aircrafts. The terminal facilities were provided by Department of Civil Aviation in a hanger which could accommodate approximately 40 passengers.

The Airport gained significant importance after the shifting of the capital from Karachi to Islamabad. Pakistan International Airlines, the National Flag carrier started its operation in 1958. Besides that CVOR has been installed during that time for Air Traffic control.

Pakistan International Airlines, the National Flag carrier started its International operation in 1963. The existing Benazir Bhutto International Airport is a joint user airport which is being used both for Commercial and Military purposes and it was built in 1963.

In 1972, VVIP/VIP Lounges (State & Executive Lounges) and Operational Control Centre were constructed. VIPs as well as public scheduled operations for many airlines. Foreign diplomats, high level government officials, as well as military officials are welcomed at this airport.

In the year 1974, R/W 12/30 (9000x 150 ft) and 6 parking bays were prepared and Precision Approach Lighting System and ILS installed with all associated provisions of Navigational-Aids & allied equipments for commercial & non-commercial aircrafts.

Due to rapid growth in population and traffic, the airport has become severely congested. In the year 1983, Domestic Arrival, International Departure and Arrival Lounges, Concourse Hall, Cargo Area and CAA Mosque constructed to facilitate the air passenger for domestic and international operations. Personal Announcement and Flight Information Display System was introduced at the airport and DVOR has been installed.

In the year 1984, Separate Hajj Lounge was constructed for intending pilgrims to holy land for Pre and Post Hajj from Benazir Bhutto International Airport. ILS system was also upgraded during that year.

RADAR & Automatic Message Switching System Operation started in 1993 and after the extension of Runway upto 10800 feet in 1995, construction of International Departure Lounge and extension to Car Park was completed.

After the renovation of Int’l /Domestic Arrival lounges, Domestic Briefing Area & Concourse Hall was constructed in the year 2002 and in the year 2003-04 the extension & renovation of Executive (Rawal) Lounge completed and re-carpeting work on main runway carried out from 30 thresholds to 3000 feet ahead (3000 x 50 feet) on rubber deposit affected area. The extension and renovation of Int’l Briefing Area was also made in the same year.

In October 2005, Islamabad handled additional aircraft that provided aid for the devastating earthquake affected people of Azad Jammu Kashmir and Khyber Pakhtun Khawa Province. The largest, among these aircraft was the An-225 Mriya. Virgin Atlantic Airways operated a special relief flight to Islamabad using a Boeing 747 with 55 tonnes of aid. Total 13995 flights were handled at CAA Civil Apron.

The plan to construct a new airport for Islamabad was conceived in the late 1980s to deal with the problem of increased passenger load at the Benazir Bhutto International Airport (then known as the Fatima Jinnah International Airport). Over congestion at the airport impeded the entire process of passenger handling because of which chaotic scenes became a norm. The concourse hall and car parking area are packed to capacity most of the day. The current annual turnover of passengers at the current airport is about 3.5 million. It was estimated that the number of passengers at the airport is growing by 14 per cent annually compared to national air passenger growth rate of less than four per cent, making it one of the busiest airports in the country. Therefore a site in Rawalpindi district was selected as the site for its construction just a few kilometers from the Islamabad interchange on M1/M2 motorways. However the project couldn't be started and was repeatedly postponed till 2005. This finally brought the situation to the point where it could no longer absorb the rising number of passengers. Finally the plan to construct a new airport was announced on 7 January 2005 by Civil Aviation Authority (CAA). And finally the Ground Breaking Ceremony of New Islamabad International Airport (NIIA) at Rakh Pind Ranjha (Fateh Jang) road held on 7-4-2007.

In the fiscal year 2008–2009, over 3,136,664 passengers used Benazir Bhutto International Airport and 34,025 aircraft movements were registered. The airport serves as a hub for the flag carrier, Pakistan International Airlines. It is also the hub of Shaheen Air International and a focus city of Airblue. It was renamed after the late Pakistani leader Benazir Bhutto by the then Prime Minister of Pakistan, Yusuf Raza Gillani on 21st June 2008. During that time expansion of Apron for parking of B777-ER also carried out and Re-carpeting of main runway was also done.

On 28 July 2010, Airblue Flight 202, a domestic flight from Karachi operated by Airbus A321 AP-BJB, crashed into the Margalla Hills in Islamabad despite this major setback it grows and widens its operation to Middle East and Europe from BBIAP Islamabad.

On 20 April 2012, the Bhoja Air flight BHO-213 Boeing 737, flying from Jinnah International Airport, Karachi, crashed in bad weather during its approach to Benazir Bhutto International Airport, Islamabad. All 121 passengers and 6 crew members aboard were killed in the crash. This was the inaugural flight of Bhoja Air's second daily service on this route.

After the incident of 09/11, the security situation dictated authorities to focus on strengthening of security arrangements and infrastructure. CAA BBIAP, coping up the security requirements, managed well to maintain its focus on passenger facilitation along with the day-to-day requirements by the security agencies. Especially during last two years, i.e. since 2012-13, the airports had been on high alert.

In order to maintain quality and to meet International Standards, different development projects related to passenger facilitation, convenience and security related infrastructural measures have been started. Expansion & redesigning of International Briefing area, remodeling of International Departure Lounge and concourse hall is in hand. The purpose of expansion is to create more space for check-in counters which provides passenger convenience and expeditious briefing. CAA functionary car park for 300 vehicles and 200 motorcycles is also being constructed, which is situated at the Nur Khan Airbase road. All the departments i.e. CAA, ASF, PIA, Ground Handling Agencies, Immigration, Pakistan Customs, ANF, Airport Health and other International Airlines staff working at BBIAP are getting benefit from this parking lot. After the shifting of functionary car park, revamping of existing car park is in hand at BBIAP, this include the redesigning of fast track, drop lane, boundary walls and providing covered walkway throughout the length of car park which not only will facilitate the passengers / meeters & greeters in rain but also provide shelter from scorching sun light in summers, also it enhance the overall look of the car park.