The Goddard Space Flight Center's Flight Operations Team will operate the Aura spacecraft. Flight operations are the "mission control" of a satellite mission. The Operations Team tracks and controls Aura to keep it in its designated orbit and monitor health and safety of the spacecraft and its instruments.

The team commands and controls the instruments on the spacecraft in order to meet the data acquisition requirements of the ground stations. The team also coordinates observations from multiple instruments, provides mission timelines, and develops and implements contingency plans.

Aura is tracked through a network of ground stations and satellites known as TDRSS (Tracking and Data Relay Satellite System). Data are downlinked to polar ground stations in Norway and Alaska. The Flight Operations Team also interacts with NASA's international partners' instrument control centers for exchange of planning and command and control information.