We develop a mechanistic model for post-operative pain and apply it to describe the pharmacodynamic effects of the kappa-opioids nalbuphine and naloxone administered either alone or in combination in patients after surgical removal of one or more madibular third molar teeth. Data were obtained from 6 clinical studies in which a total of 304 patients were intravenously administered single doses of 2.5, 5, 10 or 20 mg of nalbuphine. Some groups also received 0.2 or 0.4 mg of naloxone. A total of 3,040 Visual analog scale (VAS) pain ratings were recorded at 20 min intervals for 3 h after drug administration. We used a two-site indirect action model to describe early and late pain and to incorporate the effect of nalbuphine and naloxone on pain over time. A mixed effects statistical model was used to account for inter- and intra-individual variability. Our model estimated the population average baseline pain score in men to be lower than that in women (68 vs. 76 mm on the 100 mm VAS scale). The model confirmed a late increase in pain (anti-analgesia) and estimated the lag time for the start of anti-analgesia to be 73 min after study drug administration. The maximum early phase pain score is 81.6 mm while the maximum anti-analgesia is 16.1 mm. The nalbuphine dose required to reduce early pain by 50% (ED(50)) was estimated to be 5.85 mg and the naloxone dose required to reduce late phase pain by 50% was estimated to be 0.5 mg. The model confirmed the results from conventional statistical analyses performed previously on individual studies.