PurposeScreening programs using fecal occult blood testing help reduce mortality from colorectal cancer (CRC). Colonoscopy and colonoscopy combined with fecal occult blood testing are considered alternatives with higher sensitivity than fecal tests; however, to our knowledge, randomized controlled trials (RCTs) providing such evidence have not been reported. Therefore, this study aimed to compare screening using the fecal immunochemical test (FIT) combined with colonoscopy and FIT alone to evaluate the efficacy of colonoscopy screening in reducing CRC mortality.MethodsThis multicenter, prospective, randomized, controlled study included average-risk individuals for CRC living in the study areas and aged 40–74 years. The exclusion criteria were history of CRC, hereditary non-polyposis CRC, familial adenomatous polyposis, inflammatory bowel diseases, history of cancer other than CRC within the past 5 years, and not expected to survive from comorbid illness. The intervention group underwent one-time colonoscopy and annual FIT, while the control group underwent annual FIT. The primary endpoint was mortality from CRC, while the secondary endpoints were cumulative incidence of invasive CRC, advanced CRC (invasion into the muscle layer or deeper), invasive cancer and screening sensitivities and specificities of invasive CRC, whole CRC, advanced neoplasia, and prevalence of adverse events. The intervention and control groups comprised 4876 and 4875 participants, respectively.ConclusionThis explanatory RCT evaluated the efficacy of colonoscopy screening by valid statistical inference based on randomization. Data on adverse events from this kind of screening are necessary when considering implementation of future screening programs.Trial registrationUMIN Clinical Trials Registry, number UMIN000001980.