Continuous monitoring of cerebral blood oxygenation is critically important for successful treatment of patients with severe traumatic brain injury. At present, the techniques for monitoring blood oxygenation are invasive. Recently we proposed noninvasive monitoring of cerebral blood oxygenation by using optoacoustic probing of blood circulating in the internal jugular vein (IJV). A major source of error in the optoacoustic measurement with a single-element optoacoustic probe is the spatial misalignment between the probe and the IJV. We built a LabView®-based scanning system that automatically moves our optoacoustic probe across the IJV while continuously taking measurements. Automatic signal processing determines the signal with the best probe-vessel alignment which then is used for further processing. The scanning system was tested in phantoms using solutions with different absorption coefficients and with blood with various levels of blood oxygenation. Amplitudes and profiles of the optoacoustic signals recorded from the phantoms closely followed the blood oxygenation changes in accordance with blood optical properties. These data indicate that the scanning system is capable of improving the accuracy of non-invasive monitoring of blood oxygenation by minimizing errors associated with lateral misalignment of the probe with respect to blood vessels.