Background: This study aimed to explore the role of a non-synonymous single-nucleotide polymorphism, 3312G>T, in SCN9A, which was identified in probands with congenital indifference to pain, but which is also present in normal controls, in the prediction of individual baseline pain perception, and postoperative pain sensitivity in the general population. Methods: Preoperative pressure pain thresholds and tolerance were measured in 200 patients undergoing pancreatectomy, and the postoperative pain sensitivity and analgesic demand were recorded. These variables were compared according to the SCN9A 3312G>T alleles. Logistic regression analysis was used to test the role of preoperative variables in the prediction of postoperative inadequate analgesia. Results: The 3312Tallele was present in 22 individuals, and the 3312Tallele frequency was 5.5% (22/200). The average patient-controlled analgesia pressing frequency and opioid consumption in 3312G patients was significantly higher than those in 3312T patients (2.70 [SD: 0.84] vs. 2.05 [SD: 0.43], P < 0.001; 100.8 [SD: 40.7] vs. 74.8 [SD: 20.8] ml, P = 0.006). The incidence of inadequate analgesia in 3312G patients was significantly higher than that of patients carrying the 3312Tallele (29.2% vs. 4.5%; P = 0.013). Carrying the 3312Tallele and having a higher pressure pain threshold predicted a lower risk of postoperative inadequate analgesia, with an odds ratio of 0.10 (95% CI: 0.01 to 0.76, P = 0.026) and 0.32 (95% CI: 0.13 to 0.82, P = 0.018), respectively. Conclusion: Patients carrying the SCN9A 3312Tallele presented with lower postoperative pain sensitivity in the presence of a similar surgical pain stimulus, and had a lower likelihood of developing inadequate analgesia than those carrying the 3312Gallele.