Safety-critical applications require controllers/policies that can guarantee safety with high confidence. The control barrier function is a useful tool to guarantee safety if we have access to the ground-truth system dynamics. In practice, we have inaccurate knowledge of the system dynamics, which can lead to unsafe behaviors due to unmodeled residual dynamics. Learning the residual dynamics with deterministic machine learning models can prevent the unsafe behavior but can fail when the predictions are imperfect. In this situation, a probabilistic learning method that reasons about the uncertainty of its predictions can help provide robust safety margins. In this work, we use a Gaussian process to model the projection of the residual dynamics onto a control barrier function. We propose a novel optimization procedure to generate safe controls that can guarantee safety with high probability. The safety filter is provided with the ability to reason about the uncertainty of the predictions from the GP. We provide a proof-of-concept on a Segway platform. The probabilistic approach is able to reduce the number of safety violations by 50% compared to the deterministic approach with a neural network.