Carpenter entered the U.S. Navy in 1949 and served in the Korean War. He had been a Navy test pilot and had attended the Naval Air Intelligence School in 1958. He was one of seven men selected in April 1959 for the National Aeronautics and Space Administration's Project Mercury. In 1964 he broke his left arm in a motorcycle accident. The resultant inability to rotate his arm properly forced his removal from spaceflight status.

In 1965 Carpenter was detached from the space program to lead two teams in the Sealab II experiment, living and working 205 feet (62.5 metres) under the Pacific Ocean as part of the U.S. Navy's effort to find better rescue methods for submarines. In 1967 he helped set up Sealab III but retired from naval duty in 1969 to enter private oceanography and energy research.