Radiometric infrared (IR) imaging is a valuable technique for remote-sensing applications in precision agriculture, such as irrigation monitoring, crop health assessment, and yield estimation. Low-cost uncooled non-radiometric IR cameras offer new implementations in agricultural monitoring. However, these cameras have inherent drawbacks that limit their usability, such as low spatial resolution, spatially variant nonuniformity, and lack of radiometric calibration. In this article, we present an end-to-end pipeline for temperature estimation and super resolution of frames captured by a low-cost uncooled IR camera. The pipeline consists of two main components: a deep-learning-based temperature-estimation module, and a deep-learning-based super-resolution module. The temperature-estimation module learns to map the raw gray level IR images to the corresponding temperature maps while also correcting for nonuniformity. The super-resolution module uses a deep-learning network to enhance the spatial resolution of the IR images by scale factors of x2 and x4. We evaluated the performance of the pipeline on both simulated and real-world agricultural datasets composing of roughly 20,000 frames of various crops. For the simulated data, the results were on par with the real-world data with sub-degree accuracy. For the real data, the proposed pipeline was compared to a high-end radiometric thermal camera, and achieved sub-degree accuracy. The results of the real data are on par with the simulated data. The proposed pipeline can enable various applications in precision agriculture that require high quality thermal information from low-cost IR cameras.