The acquisition, processing, and interpretation of thermal images from unmanned aerial vehicles (UAVs) is becoming a useful source of information for agronomic applications because of the higher temporal and spatial resolution of these products compared with those obtained from satellites. However, due to the low load capacity of the UAV they need to mount light, uncooled thermal cameras, where the microbolometer is not stabilized to a constant temperature. This makes the camera precision low for many applications. Additionally, the low contrast of the thermal images makes the photogrammetry process inaccurate, which result in large errors in the generation of orthoimages. In this research, we propose the use of new calibration algorithms, based on neural networks, which consider the sensor temperature and the digital response of the microbolometer as input data. In addition, we evaluate the use of the Wallis filter for improving the quality of the photogrammetry process using structure from motion software. With the proposed calibration algorithm, the measurement accuracy increased from 3.55 °C with the original camera configuration to 1.37 °C. The implementation of the Wallis filter increases the number of tie-point from 58,000 to 110,000 and decreases the total positing error from 7.1 m to 1.3 m.