Persistent exposure to highly pulsatile blood can damage the brain’s microvasculature. A convenient method for measuring cerebral pulsatility would allow investigation into its relationship with vascular dysfunction and cognitive decline. In this work, we propose a convolutional neural network (CNN) based deep learning solution to estimate cerebral pulsatility using only the frequency content from BOLD MRI scans. Various frequency component inputs were assessed, and echo time dependence was evaluated with a 5-fold cross-validation. Pulsatility was estimated from BOLD MRI data acquired on a different scanner to assess generalizability. The CNN reliably estimated pulsatility and was robust to various scan parameters.