The nucleic acid base method is a widely used method in foodborne pathogen detection as a rapid method and confirmation of traditional methods. This method is simply hybridizing the target region sequence of a foodborne pathogen with a synthetic oligonucleotide (probes or primers), and the prediction of this primer or probe is a critical step that needs more care. Hence Proper validation of the application used for this prediction is important. In this paper, we validate FBPP application by the evaluation of the predicted primers takes place at the three levels: genus level by using the Inv A gene for all salmonella species; species level by using the HipO gene for only Campylobacter jejuni species; and serotype level through the O antigen flippase gene for Escherichia coli O157:H7. It includes measures of inclusivity (detection of the target microorganism) and exclusivity (non-detection of non-target microorganisms) as recommended for the performance characteristics of the PCR-based method (ISO 22118). Furthermore, the sequence of the PCR product has been verified to confirm the correct PCR product has been amplified. The results demonstrate the ability of FBPP to create useful primers for foodborne pathogens under the three levels of evaluation.