Onboard cloud segmentation is a critical yet underexplored task in thermal Earth observation (EO), particularly for CubeSat missions constrained by limited hardware and spectral information. CubeSats often rely on a single thermal band and lack sufficient labeled data, making conventional cloud masking techniques infeasible. This work addresses these challenges by applying transfer learning to thermal cloud segmentation for the XXXX CubeSat (name redacted for review), using a UNet with a lightweight MobileNet encoder. We pretrain the model on the public Landsat-7 Cloud Cover Assessment Dataset and fine-tune it with a small set of mission-specific samples in a joint-training setup, improving the macro F1 from 0.850 to 0.877 over XXXX-only baselines. We convert the model to a TensorRT engine and demonstrate full-image inference in under 5 seconds on an NVIDIA Jetson Nano. These results show that leveraging public datasets and lightweight architectures can enable accurate, efficient thermal-only cloud masking on-orbit, supporting real-time decision-making in data-limited EO missions.