Gender classification has found many useful applications in the broader domain of computer vision systems including in-cabin driver monitoring systems, human–computer interaction, video surveillance systems, crowd monitoring, data collection systems for the retail sector, and psychological analysis. In previous studies, researchers have established a gender classification system using visible spectrum images of the human face. However, there are many factors affecting the performance of these systems including illumination conditions, shadow, occlusions, and time of day. Our study is focused on evaluating the use of thermal imaging to overcome these challenges by providing a reliable means of gender classification. As thermal images lack some of the facial definition of other imaging modalities, a range of state-of-the-art deep neural networks are trained to perform the classification task. For our study, the Tufts University thermal facial image dataset was used for training. This features thermal facial images from more than 100 subjects gathered in multiple poses and multiple modalities and provided a good gender balance to support the classification task. These facial samples of both male and female subjects are used to fine-tune a number of selected state-of-the-art convolution neural networks (CNN) using transfer learning. The robustness of these networks is evaluated through cross validation on the Carl thermal dataset along with an additional set of test samples acquired in a controlled lab environment using prototype uncooled thermal cameras. Finally, a new CNN architecture, optimized for the gender classification task, GENNet, is designed and evaluated with the pretrained networks.