Foodborne diseases caused by food-borne pathogen have become a global public health problem. Rapid and accurate detection of food-borne pathogenic microorganisms has become a key to the prevention and control of food-borne diseases and is also the key technology to ensuring food safety. Surface-enhanced Raman spectroscopy (SERS), as a powerful and attractive analytical tool, has the advantages of simplicity, rapidness and high sensitivity. This review summarizes the recent trends and developments of SERS in the detection of food-borne pathogenic microorganisms. A brief tutorial on SERS, the SERS enhancement theory and SERS enhancement substrate are given first of all. Then we summarize the recent trends and developments of SERS applied to the detection of foodborne pathogen in food and medical diagnosis. In addition, microfluidic SERS platforms for foodborne pathogen are discussed as well. In the field of food safety analysis, SERS combined with pattern recognition methods can rapidly and effectively identify common food-borne pathogenic microorganisms. Some studies have reported to apply SERS to detect food-borne pathogenic microorganisms in different food samples, which demonstrates the advantage of SERS as “fingerprint”. In medical diagnosis, SERS can rapidly detect food-borne pathogenic microorganisms in pathological samples (such as blood and urine). The application of SERS makes the rapid diagnosis of food-borne diseases possible due to the shortening of the sample analysis time. With the development of microfluidic technology, microfluidic platform combined with SERS technology is called “chip lab”, which can improve the controllability, stability, specificity and sensitivity for detection of food-borne pathogenic microorganisms. The review summarized and compared these different studies of SERS methods, which could be used to detect food-borne pathogenic microorganisms based on different isolation methods, different substrates or different target capture methods. These researches have demonstrated that the application of SERS in foodborne pathogenic microorganisms could overcome the shortcomings of traditional methods, and provide an effective, rapid and sensitive analytical tool for real-time monitoring of food safety and diagnosis of foodborne diseases. At the same time, there are still great challenges for the application of SERS technology in foodborne pathogenic microorganism analysis. (1) Most researches do not focus on the actual samples. However, there is really difference between the standard culture medium and the actual samples for SERS analysis. (2) There are differences between the results of different methods, mainly due to the difference of SERS substrate, the difference of the target adsorption modes, the difference of stability and so on. So further studies are needed for optimization conditions. (3) It is expected to establish standardized SERS methods to replace the traditional techniques, which could fully show the advantages of SERS including rapidness, sensitivity and simplicity. An outlook of the work done and a perspective on the future directions of SERS as a reliable and rapid analytical tool are given for a broader application prospect in food safety, biomedicine and other fields in the future.