This complex was built as part of the U.S. Navy's Trident II submarine-launch missile development effort.

On January 27, 1999, the Athena I lifted off with Taiwan's first satellite, ROCSAT-1, carrying experimental communications, ocean imagery, and ionospheric studies instruments.

[5] In early 2014, Space Florida contracted with Alliant Techsystems (ATK) to begin phase three of the communications infrastructure refurbishment, with completion expected to take one year.

[9] On July 2, 2019, NASA launched a repurposed Peacekeeper missile from SLC-46, carrying the Orion spacecraft for the Ascent Abort-2 mission.

Astra's Rocket 3.3 vehicle (serial number LV0010) carrying two TROPICS CubeSats for NASA failed to reach orbit and the satellites were lost.