In 1988, she began working at the NASA Ames Research Center as Vice President of Overset Methods, Inc. where she did Computational fluid dynamics (CFD) research on Vertical/Short Takeoff and Landing concepts. Chawla held a Certificated Flight Instructor rating for airplanes, gliders and Commercial Pilot licenses for single and multi-engine airplanes, seaplanes and gliders. In 1994, NASA selected Kalpana as an astronaut, out of more than 2000 applicants and it also provided training. Her first space mission began on November 19, 1997, as part of the six-astronaut crew that flew the Space Shuttle Columbia flight STS-87. Chawla was the first Indian-born woman and the second Indian person to fly in space, following cosmonaut Rakesh Sharma who flew in 1984 on the Soyuz T-11.
In 2000 she was selected for her second flight as part of the crew of STS-107. This mission was repeatedly delayed due to scheduling conflicts and technical problems such as the July 2002 discovery of cracks in the shuttle engine flow liners. The career graph of Kalpana reached its peak when she flew on STS-107 Columbia which spent 16 days in orbit from January 16 to February 1, 2003. Chawla's responsibilities included the microgravity experiments, for which the crew conducted nearly 80 experiments studying earth and space science, advanced technology development and astronaut health and safety.