Functional near infrared spectroscopy (fNIRS) can separately measure spatially differentiated brain functions by appropriately positioning irradiation and detection probes on the scalp, where brain region that could be assessed is limited to the adjacent region directly below the probe pair. A key challenge is determining the appropriate probe position for measuring the function of target brain region. Here, we propose an fNIRS probe positioning system using augmented reality technology. From a subject’s anatomical 3D magnetic resonance images, geometry of the head tissues including the appropriate position directly above the targeted brain region was obtained. The system captured an image of the subject’s head and several facial landmarks were extracted. Subsequently, the anatomical geometry was fitted into the captured image of the head to align with the landmark positions. Finally, the target probe positions were indicated icons on the captured head images. These were processed in real-time, while following the motion of the subject’s head. Therefore, the appropriate probe position was spatially determined by taking a video of the subject's head from various directions. The system was implemented on a generic tablet computer. Positioning accuracy of system in a mannequin head with a shape and color similar to that of a human face was assessed. Errors from the appropriate position were less than 10 mm, which is adequate for appropriate probe positioning in hemodynamic response measurement from the target gyrus, since brain gyri in human adults are approximately 10 mm in width.