After graduating, he became the assistant of Benjamin A. Gould. Gould was director of the Longitude Department of the U.S. Coast Survey program, a geodetic survey program. When Gould left to become director of the national observatory in Argentina, Chandler also left and became an actuary. However, he continued to work in astronomy as an amateur affiliated with Harvard College Observatory. Chandler is best remembered for his research on what is today known as the Chandler wobble. His research on this spanned nearly three decades.
Chandler also made contributions to other areas of astronomy, including variable stars. He independently co-discovered the nova T Coronae Borealis, improved the estimate of the constant of aberration, and computed the orbital parameters of asteroids and comets.