After earning her doctorate, which led to a patent, Dr. Ochoa joined Sandia National Laboratories as a Member of Technical Staff, where she was a co-inventor on two more patents for hybrid optical and digital image processing systems (1985 – 1988). She then joined NASA Ames Research Center in Mountain View, CA, as a Group Leader before being promoted after five months to Chief of the Intelligent Systems Technology Branch. Dr. Ochoa led research and development in space-based computing systems with the Research Center, overseeing a group of 30 engineers and scientists. In 1990, Dr. Ochoa was selected as a NASA Astronaut; in 1993, she flew on her first mission, becoming the first Latina woman to go to space. Over her 17-year career as an Astronaut, she would spend 41 days in space, including four Space Shuttle flights. Her roles on her missions included serving as payload commander, flight engineer, and lead robotic arm operator. Between her missions, she directed the Astronaut Office Support of the International Space Station (ISS), which included collaboration and negotiation with international space agencies, led astronauts working in Mission Control supporting space shuttle missions, and defined new training and operations requirements for operations on ISS—furthermore, Dr. Ochoa. Dr. Ochoa served as the Deputy Director and later Director of Flight Crew Operations at NASA Johnson Space Center (2002-2007), including through the aftermath of the Space Shuttle Columbia disaster (2003).

In 2007, Dr. Ochoa was selected as the Deputy Center Director of NASA Johnson Space Center, where she would contribute to completing the International Space Station assembly and the Space Shuttle Program. She also worked on a new program management development course and served on the inclusion and innovation council. Dr. Ochoa was promoted to Director of the Johnson Space Center in 2013, becoming the 11th Director - the first Hispanic and second female. Under her leadership, the organization adopted a simplified process to develop experimental flight hardware and a streamlined organizational structure. It expanded the use of open innovation and partnerships, including with energy and medical companies. Dr. Ochoa served as Director for five and a half years.

Dr. Ochoa has received numerous accolades for her work with NASA and contributions to science and technology, including NASA's highest honor, the Distinguished Service Medal in 2003 and 2018. She was inducted into the United States Astronaut Hall of Fame in 2017 and was recognized in Hispanic Executive's Best of the Boardroom issue the same year. In 2018, Dr. Ochoa was inducted into the International Air and Space Hall of Fame, and in 2019, she was inducted into the National Academy of Engineering. She is a fellow of the American Association for the Advancement of Science (AAAS), the American Institute of Aeronautics and Astronautics (AIAA), the National Academy of Inventors (NAI), and the Optical Society of America (OSA). She is honored to have seven schools named after her and has received eight honorary doctorates for her work both in space and on the ground.

In 2018, Dr. Ochoa retired from NASA. She serves on several boards, continues outreach through speaking engagements and bilingual children's books, and concluded a term as Chair of the National Science Board in 2022. Dr. Ochoa also plays the flute in community groups in Boise, where she now resides. Though she has many career highlights and accomplishments, Dr. Ochoa highlights being selected as an astronaut, flying on four Space Shuttle Missions, and holding various leadership positions at the Johnson Space Center as accomplishments she is most proud of.