Rapid and sensitive detection of food-borne pathogens is critical for food safety from the viewpoint of both the public health professionals and the food industry. Conventional method is, however, known to be labor-intensive, time-consuming, and expensive due to the separate cultivation and biochemical assay. Many relevant technologies, such as flow cytometry, MALDI-MS, ESI-MS, DNA microarray, and CE, have been intensively developed to date. Among them, CE is considered to be the most efficient and reproducible because of low sample loss and simple automation. CE-based pathogen detection methods can be classified into three categories based on the separation targets: cell separation, nucleic-acid-based identification, and protein separation coupled with characterization. In this review, recent developments in each sphere of CE-based technology are discussed. Additionally, the critical features of each approach and necessary future technical improvements are also reviewed.