Canopy temperature is an important variable directly linked to a plants water status. Recent advances in Unmanned Aerial Vehicle (UAV) and sensor technology provides a great opportunity to obtain high-quality imagery for crop monitoring and high-throughput phenotyping (HTP) applications. In this study, a UAV-based thermal system was developed to directly measure canopy temperature, skipping the traditional radiometric calibration process which is time-consuming and complicates data processing. Raw thermal imagery collected over a cotton field was converted to surface temperature using the Software Development Kit (SDK) provided by the sensor company. Canopy temperature map was generated using Structure from Motion (SfM), and Thermal Stress Index (TSI) was calculated for the test site. UAV temperature measurements were compared to ground measurements acquired by net radiometers and thermocouples. Temperature differences between UAV and ground measurements were less than 5%, and UAV measurements proved to be more stable. The proposed UAV system was successful in showing temperature differences between the cotton genotype. In conclusion, the system described in this study could possibly be used to monitor crop water status in a field setting, which should prove helpful for precision agriculture and crop research.