Abstract Background Public health events caused by foodborne virus cause huge economic and social burden to the affected countries. Foodborne virus detection in food is a very arduous task due to its trace amounts and interference by complex food matrix components. Conventional techniques face a number of drawbacks, such as time-consuming, laborious and often require skilled technicians. This represents an interesting challenge for microfluidic technologies, from on-chip sample separation as well as for integrity perspective. Scope and approach The focus of this review is to highlight the integrated microfluidic system for nucleic acid-based foodborne virus analysis, including sample preparation, on-chip nucleic acid amplification, on-chip detection, system integration and automation. Finally, challenges and future perspectives of practical application of this technology were further discussed. Key findings and conclusions Microfluidic technology has provided a new platform for rapid and effective detection of foodborne virus. The low sample/reagent volume consumption and the integration of detection make microfluidic technology an ideal choice for on-site use and more convenience to food safety supervision department.