Background: In Flanders, the uptake in the population-based colorectal cancer (CRC) screening program (using fecal immunochemical test, FIT) is suboptimal (~50%). This study explored the reasons for inconsistent participation in FIT screening among irregular participants in Flanders. Methods: An online survey with both open questions and fixed statements was sent to irregular participants (2016–2018) in the Flemish CRC screening program. A reminder email followed eight weeks after the first email. Data analysis used both qualitative and quantitative approaches. Post-stratification weights based on gender, age group, and the first two digits of the postcode were employed to reduce non-response bias. Results: In total, 5328 out of 19,592 irregular participants responded to the survey. While the main reasons not to participate were related to ‘postponing participation’ and ‘having other priorities’, the main reasons to participate were related to the importance of (preventive) health checks. The role of general practitioners (GPs) in promoting CRC screening also emerged as an important theme among the respondents’ answers (based on fixed statements). Conclusions: The study reported the main reasons for inconsistent participation in FIT screening for CRC in Flanders. The findings are helpful in guiding tailored interventions to increase FIT screening uptake in the region.