We have built an Atmospheric Transmission Monitoring Camera (aTmCam), which consists of four telescopes and detectors each with a narrow-band filter that monitors the brightness of suitable standard stars. Each narrowband filter is selected to monitor a different wavelength region of the atmospheric transmission, including regions dominated by the precipitable water vapor and aerosol optical depth. The colors of the stars are measured by this multi narrow-band imager system simultaneously. The measured colors, a model of the observed star, and the measured throughput of the system can be used to derive the atmospheric transmission of a site on sub-minute time scales. We deployed such a system to the Cerro Tololo Inter-American Observatory (CTIO) and executed two one-month-long observing campaigns in Oct-Nov 2012 and Sept-Oct 2013. We have determined the time and angular scales of variations in the atmospheric transmission above CTIO during these observing runs. We also compared our results with those from a GPS Water Vapor Monitoring System and find general agreement. The information for the atmospheric transmission can be used to improve photometric precision of large imaging surveys such as the Dark Energy Survey and the Large Synoptic Survey Telescope.