Her career in astronomy began when she demonstrated good stereoscopic vision, a particularly valuable quality for looking for objects in near-Earth space.

Despite the fact that her degrees were not in science, having that visual ability motivated the California Institute of Technology (Caltech) to hire her as a research assistant on a team led by her husband.

[5] When her brother attended Caltech, his roommate was a young graduate student named Eugene "Gene" Shoemaker.

When Shoemaker returned to his studies at Princeton, Carolyn and he maintained a pen pal relationship and later both attended a two-week camping trip on the Cumberland Plateau.

[3] Mary Chapman, author of Shoemaker's biography for the USGS Astrogeology Center, wrote "Carolyn is a warm, caring, and extremely patient woman, but her skills were better suited for a non-teaching environment.

[2] However, she reportedly told others that, "listening to Gene explaining geology made what she had thought was a boring subject into an exciting and interesting pursuit of knowledge".

[6] Teamed with astronomer David H. Levy, the Shoemakers identified Shoemaker-Levy 9, a fragmented comet with an orbit that intersected that of Jupiter, on March 24, 1993.

[11][12] In the 1980s and 1990s, Shoemaker used film taken at the wide-field telescope at the Palomar Observatory, combined with a stereoscope, to find objects that moved against the background of fixed stars.

[2] Following recovery from the injuries she suffered in the 1997 automobile crash in which her husband was killed, she resumed her work at the Lowell Observatory with Levy.

[15] The Carolyn Shoemaker formation within Gale crater, forms part of the broader Mount Sharp group was named after her.