The E and B Experiment (EBEX) is a balloon-borne telescope designed to probe polarization signals in the CMB resulting from primordial gravitational waves, gravitational lensing, and Galactic dust emission. EBEX completed an 11 day flight over Antarctica in January 2013 and data analysis is underway. EBEX employs two star cameras to achieve its real-time and post-flight pointing requirements. We wrote a software application called STARS to operate, command, and collect data from each of the star cameras, and to interface them with the main flight computer. We paid special attention to make the software robust against potential in-flight failures. We report on the implementation, testing, and successful in flight performance of STARS.