Transcranial MRI-guided focused ultrasound (TcMRgFUS) thermal ablation is a noninvasive functional neurosurgery technique. Previous reports have shown that damage in the skull bone marrow can occur at high acoustic energies. While this damage is asymptomatic, it would be desirable to avoid it. Here we examined whether acoustic and thermal simulations can predict where the thermal lesions in the marrow occurred. Post-treatment imaging was obtained at 3-15 months after 40 clinical TcMRgFUS procedures, and bone marrow lesions were observed after 16 treatments. The presence of lesions was predicted by the acoustic energy with a threshold of 18.1-21.1 kJ (maximum acoustic energy used) and 97-112 kJ (total acoustic energy applied over the whole treatment). The size of the lesions was not always predicted by the acoustic energy used during treatment alone. In contrast, the locations, sizes, and shapes of the heated regions estimated by the acoustic and thermal simulations were qualitatively similar to those of the lesions. The lesions generally appeared in areas that were predicted to have high temperatures. While more work is needed to validate the temperature estimates in and around the skull, being able to predict the locations and onset for lesions in the bone marrow could allow for better distribution of the acoustic energy over the skull. Understanding skull absorption characteristics of TcMRgFUS could also be useful in optimizing transcranial focusing.