Rehabilitation work on the lower interchange was last undertaken in 2012 with the reconfiguration of an off-ramp to improve access to Ninoy Aquino International Airport and the strengthening of the Sales Bridge[2] brought about by the number of vehicles using the interchange.

[5] Construction of the upper interchange was recommended in the Metro Manila Urban Transportation Integration Study (MMUTIS), commissioned by the Japan International Cooperation Agency (JICA) in 1999, as a solution to worsening traffic congestion into and out of the airport.

On July 17, 2001, President Gloria Macapagal Arroyo and her Cabinet approved the construction of the NAIA Expressway, funded through a Japanese loan package,[7] and construction of the upper interchange began on March 17, 2004.

[8] The ₱1 billion interchange, which was built in four parts, was inaugurated by President Arroyo and other officials on May 30, 2009.

The upper interchange was free of charge until November 16, 2011, when tolls began to be collected by Citra Metro Manila Tollways Corporation (CMMTC), the concessionaire of the Skyway system.