Background Colorectal cancer (CRC) incidence and mortality are increasing in many middle- and lower-income countries, possibly due to a combination of changing lifestyles and improved healthcare infrastructure that facilitates diagnosis. Unfortunately, a large proportion of cases may be diagnosed at advanced stages, resulting in poor outcomes. Decreasing trends in higher income countries are likely due to improved early detection combined with best practices in CRC treatment and management. More data on implementation of better quality CRC screening programs are needed for contexts where incidence is increasing. Therefore, we sought to identify potential barriers and facilitators for future implementation of fecal immunochemical test (FIT)-based CRC screening in a public healthcare system in a middle-income country with increasing CRC incidence and mortality. Methods. Qualitative study including semi-structured individual and focus group interviews with different stakeholders of colorectal cancer screening: 30 average-risk lay people, 13 health care personnel from a local public clinic, and 7 endoscopy unit personnel from a cancer referral hospital. All interviews were transcribed verbatim for analysis. Data was analyzed using the constant comparison method, under the theoretical perspectives of the Social Ecological Model (SEM), the PRECEDE-PROCEED Model, and the Health Belief Model. Results. We found multiple barriers and facilitators for implementation of a FIT-based CRC screening program at different levels of the SEM. The main barriers in each of the SEM levels, were: 1) at the social context level: poverty, health literacy and lay beliefs related to gender, cancer, allopathic medicine, and religion; 2) at the health services organization level: the lack of CRC knowledge among health care personnel and the community perception of poor quality of health care; 3) at the individual level: a lack of CRC awareness and therefore lack of risk perception, together with fear of participating in screening activities and finding out about a serious disease. The main facilitators perceived by the participants were CRC screening information and the free provision of screening tests.Conclusions. This study’s findings suggest the need for a multi-level CRC screening program that includes complementary strategies aimed at reducing perceived barriers and enhancing facilitators, starting with: 1) free provision of screening tests, 2) education of primary health care personnel, and 3) promotion of non fear-based CRC screening awareness among the target population, taking into account their lay beliefs.