Background: A timely diagnostic colonoscopy (DC) after a positive FIT result is crucial for effective colorectal cancer (CRC) screening. In the Flemish CRC screening program (CRC-SP), 17% of FIT-positive participants had no DC in 2020. This study explores self-reported barriers, experiences, and perceptions about DC in FIT-positive participants. Methods: An online survey combining qualitative and quantitative approaches was sent by email to FIT-positive participants (November 2019–September 2020). Results: Out of 5134 invitees, 1597 respondents (31.1%) completed the survey. Among them, 77.5% had undergone/planned a DC, while 22.5% were unwilling to undergo a DC. DC perceptions, expectations, and experiences differed among groups; 57% of the ‘DC-performed’ group reported better-than-expected experiences. A substantial portion of the ‘DC-naïve’ group anticipated pain (42%) and embarrassment (30%), while the actual experience in the ‘DC-performed’ group was much lower (6.4% and 3.2%, respectively). GP advice, support from close contacts, and colonoscopy experiencers trigger DC planning, whereas lack of symptoms, false-positive perception, fears, and embarrassment were identified as barriers to DC. Conclusions: The study reveals barriers/facilitators for a DC in the Flemish CRC-SP. The findings inform targeted interventions for improved DC completion and its impact, including patient navigation and testimonial videos of ‘colonoscopy experiencers’ to address DC misperceptions.