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Abstract Background A pulse oximeter is one of the most important monitors to save patients undergoing anesthesia and monitored sedation. The authors report a case of orthopedic surgery, in which interference of pulse oximetry occurred when using a Stealth Station™ navigation system (Medtronic Sofamor Danek, Memphis, TN). Applying a black plastic shield (Masimo Ambient Shield: Masimo Corporation, Irvine, CA) completely eliminated the interference. Case presentation A 37-year-old male patient with a giant cell tumor of the left femur was scheduled to undergo curettage of the femur using an intraoperative CT three-dimensional imaging system (O-arm™) and Stealth Station™ navigation system. During the surgery, the SpO2 value, which was maintained between 97 and 99% until the time, disappeared suddenly with abnormal pulse wave. Because a distortion in the SpO2 value was reproduced by repeated movement of cameras on the head of the Stealth Station™ navigation system, we recognized that the interference signal was coming from the navigation system. To eliminate the infrared light, the pulse oximetry probe was covered with a black plastic shield and the interference was completely eliminated. Conclusions The Stealth Station™ navigation system was found to interfere with the SpO2 value, and a black plastic shield was useful for eliminating the interfering signal. Anesthesiologists should understand the risk of interference by the neuro-navigation system and know how to solve the problem.