Background and study aims Female sex has been identified as a factor increasing patients’ pain during colonoscopy. The aim of this randomized controlled study was to investigate the efficacy of a small-caliber colonoscope, PCF-PQ260 L, for limiting pain in women during unsedated colonoscopy. Patients and methods Women who underwent unsedated colonoscopy were randomly allocated to either the small-caliber or standard colonoscope group. The primary outcome was overall pain and secondary outcomes were maximum pain and procedural measures. In addition, the effects of colonoscope type were analysed using analysis of covariance and logistic regression with adjustment for stratification factors, age and prior abdomino-pelvic surgery. Results A total of 220 women were randomly assigned to the small-caliber (n = 110) or standard (n = 110) colonoscope groups. Overall and maximum pain scores were significantly lower in the small-caliber colonoscope group than the standard colonoscope group (overall pain, 20.0 vs. 32.4, P < 0.0001; maximum pain, 28.9 vs. 47.2, P < 0.0001). The small-caliber colonoscope group achieved a superior cecal intubation rate (99 % vs. 93 %, P = 0.035). The rate of patient acceptance of unsedated colonoscopy in the future was higher in the small-caliber colonoscope group than in the standard colonoscope group (98 % vs. 87 %, P = 0.003). In addition, the small-caliber colonoscope was superior with respect to reducing pain and improving the rate of patient acceptance of unsedated colonoscopy with adjustment. Conclusions This study demonstrates the efficacy of the small-caliber colonoscope for reducing pain in women and improving their rate of acceptance of unsedated colonoscopy.