Objective The national population-based colorectal cancer screening programme in Hungary was initiated in December 2018. We aimed to evaluate the current programme and investigate the costs and benefits of potential future changes to overcome the low coverage of the target population. Methods We performed an economic evaluation from a healthcare payer perspective using an established micro-simulation model (Microsimulation Screening Analysis-Colon). We simulated costs and benefits of screening with fecal immunochemical test in the Hungarian population aged 50–100, investigating also the impact of potential future scenarios which were assumed to increase invitation coverage: improvement of the IT platform currently used by GPs or distributing the tests through pharmacies instead of GPs. Results The model predicted that the current screening programme could lead to 6.2% colorectal cancer mortality reduction between 2018 and 2050 compared to no screening. Even higher reductions, up to 16.6%, were estimated when tests were distributed through pharmacies and higher coverage was assumed. This change in the programme was estimated to require up to 26 million performed fecal immunochemical tests and 1 million colonoscopies for the simulated period. These future scenarios have acceptable cost-benefit ratios of €8000–€8700 per life-years gained depending on the assumed adherence of invited individuals. Conclusions With its limitations, the current colorectal cancer screening programme in Hungary will have a modest impact on colorectal cancer mortality. Significant improvements in mortality reduction could be made at acceptable costs, if the tests were to be distributed by pharmacies allowing the entire target population to be invited.