Purpose To study patient safety in third molar surgery, where two different doses of S-ketamine were administered for pain relief and compared to a placebo (saline). The primary focus was capillary oxygen saturation of the blood (SpO2) and secondarily, alterations in respiratory rate, blood pressure, pulse or adverse events. Methods One hundred and sixty-eight subjects were included in a randomised, placebo-controlled, double-blind trial. The two subanaesthetic study drugs were low-dose S-ketamine (0.125 mg/kg) and high-dose S-ketamine (0.25 mg/kg). Every patient was sedated with midazolam prior to infusion of the investigational drug. The teeth were surgically removed according to a routine clinical procedure, under local anaesthesia. Results Primary end-point for the safety aspects was capillary oxygen saturation (SpO2) after administration of the investigational drug was finished. A significant difference was found between the placebo and the high-dose group at that point ( p = .021), with a decrease of saturation in the high-dose group. The lowest saturation and the number of registrations of SpO2 <90% did not show any difference between groups. Oxygen supplementation was given in circa 40% of the cases with no differences between the intervention groups. No other significant differences between groups regarding saturation or respiratory rate were noted. Conclusion In this study, it was safe to use adjunct preoperative single-dose intravenous S-ketamine 0.25 mg/kg body weight for pain relief, in midazolam-sedated patients receiving third molar surgery. There were no serious adverse events or symptoms of overdose nor any clinically relevant effects on circulatory or respiratory parameters.