In this paper, we address the particularly challenging problem of calibrating a stereo pair of low resolution (80 × 60) thermal cameras. We propose a new calibration method for such setup, based on sub-pixel image analysis of an adequate calibration pattern and bootstrap methods. The experiments show that the method achieves robust calibration with a quarter-pixel re-projection error for an optimal set of 35 input stereo pairs of the calibration pattern, which namely outperforms the standard OpenCV stereo calibration procedure.