Crop monitoring is a very important area of precision agriculture and smart farming. Through an accurate monitoring, it is possible to more efficiently manage the irrigation, fertilization, and pest control. In this study, we propose aerial thermal image calibration method and thermal image processing techniques to analyze the water stress level of fruit trees under different irrigation conditions. The calibration was performed using Gaussian process regression, and it was demonstrated as an appropriate regression method because it satisfied all requirements including the residuals’ normality, independence, and homoscedasticity. In addition, an appropriate image processing technique was necessary to selectively extract only the canopy temperature from the aerial thermal images, while excluding irrelevant elements such as the soil and other objects. For the image processing techniques, three methods (Gaussian mixture model, Otsu binarization algorithm, and Otsu binarization algorithm after Gaussian blurring) were employed. The Gaussian mixture model provided the highest accuracy and stable results for the extraction of the canopy temperature. After the aerial thermal images were subjected to calibration and image processing, the degree above nonstressed canopy (DANS) water stress index was calculated for the fruit trees under different water supply conditions. The distribution of the DANS water stress index was similar to the distribution of the canopy temperature and inversely proportional to the amount of supplied water content. Therefore, we expect that the DANS water stress index, calculated using the calibration and image processing techniques proposed in this study, can be a reliable measure for the estimation of the water stress of crops for the application of aerial infrared techniques to remote sensing.