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Patient tracking is an essential part in a surgical augmented reality system for correct hologram to patient registration. Augmented reality can support a surgeon with visual assistance to navigate more precisely during neurosurgical interventions. In this work, a system for patient tracking based on infrared markers is proposed. These markers are widely used in medical applications and meet the special medical requirements such as sterilizability. A tracking accuracy of 0.76 mm is achieved when using the near field reflectivity and depth sensor of the HoloLens. On the HoloLens a performance of 55–60 fps is reached, which grants a sufficiently stable placement of the holograms in the operating room.