The aims of this study were to identify and to prioritize challenges and difficulties which impacted on the BRC system, the most popular standard in the country. The study examined the difference among subgroup of contextual factors in mean of the effectiveness. To address these objectives, the quantitative method with statistical analysis was employed. The structured questionnaire was developed drawing on knowledge from existed literature in other countries. Data were collected from food manufacturers implemented BRC systems in Thailand. Of 217 completed questionnaires, food safety managers were in agreement that five major factors that hindered the implementation of the BRC system were lack of awareness of the requirement (4.26/5), followed by lack of skill and knowledge of implementation (4.09/5), weak prerequisite programs (4.05/5), lack of education and training (3.98/5), and inadequate infrastructure and facilities (3.88/5), respectively. It could be concluded that the topmost constraints were related majorly to people and company’s infrastructure. By evaluating the firm’s effectiveness, results reported there are significant differences among subgroup of QA systems and food safety team members. The complement of ISO 9001 to HACCP contribute more effectiveness.