During the launch of Discovery on STS-124 on May 31, 2008, the pad at LC-39A suffered extensive damage, in particular to the concrete trench used to deflect the SRBs' flames.

[7] The subsequent investigation found that the damage was the result of carbonation of epoxy and corrosion of steel anchors that held the refractory bricks in the trench in place.

[9] Prior to the SpaceX lease agreement, the pad remained as it was when Atlantis launched on the final shuttle mission on July 8, 2011, complete with a mobile launcher platform.

The pad was originally going to be modified for the Ares V rocket for the Constellation program in the mid 2010s, looking identical to LC-39B with the three lightning towers.

[15] Prior to the end of the bid period, and prior to any public announcement by NASA of the results of the process, Blue Origin filed a protest with the U.S. General Accounting Office (GAO) "over what it says is a plan by NASA to award an exclusive commercial lease to SpaceX for use of mothballed space shuttle launch pad 39A".

[16] On December 12, 2013, the GAO denied the protest and sided with NASA, which argued that the solicitation contained no preference on the use of the facility as multi-use or single-use.

SpaceX originally planned to be ready to accomplish the first launch at pad 39A—of a Falcon Heavy—as early as 2015,[28] as they had architects and engineers working on the new design and modifications since 2013.

[29][23] By late 2014, a preliminary date for a wet dress rehearsal of the Falcon Heavy was set for no earlier than July 1, 2015.

[27] In the following months, the Falcon Heavy launch was delayed multiple times and eventually pushed back to February 2018.

[31] SpaceX used the former Fixed Service Structure (FSS) of the Pad 39A launch towers and initially intended to extend it above its former 350-foot (110 m) height.

[11] SpaceX planned to eventually add at least two additional levels to the FSS, to provide crew access for the Dragon 2 launches.

[35] In 2019, SpaceX began substantial modification to LC 39A in order to begin work on phase 1 of the construction to prepare the facility to launch prototypes of the large 9 m (30 ft)-diameter methalox reusable rocket—Starship—from a launch stand, which would fly from 39A on suborbital test flight trajectories with six or fewer Raptor engines.

[37] In August 2019, SpaceX submitted an Environmental Assessment for the Starship launch system at Kennedy Space Center.

[45] On February 6, 2018, Pad 39A hosted the successful liftoff of the Falcon Heavy on its maiden launch, carrying Elon Musk's Tesla Roadster car to space;[46] and the first flight of the human-rated spacecraft Dragon 2; (Demo-1) took place there on March 2, 2019.

The second Falcon Heavy flight, carrying the Arabsat-6A communications satellite for Arabsat of Saudi Arabia, successfully launched on April 11, 2019.

[53] The private American aerospace manufacturer and space transportation services company SpaceX has been the lease holder as of April 14, 2014.

[29] For military missions from Pad 39A, payloads are vertically integrated, as that is required per a launch contract with the United States Air Force.