Food safety is crucially linked to the food system, ensuring safe production, handling, and distribution to protect public health. Food allergy has been considered as a public health and food safety issue. Despite being widely regarded as a prevailing strategy for managing food allergies, strict food avoidance faces challenges due to allergen cross-contact in the food supply chain and the potential for inaccurate allergen labeling. Hence, a scientific approach to assess allergen risk in this context is imperative. In this review, a novel approach to managing food allergies, referred to as quantitative food allergen risk assessment, is presented. This discussion covered the evolving concepts and modern analytical approaches. Moreover, this review delves into the current application of quantitative food allergen risk assessment. Finally, a valuable tool for food allergen risk assessment in the food industry, Voluntary Incidental Trace Allergen Labelling (VITAL), was introduced. The establishment of a globally harmonized and standardized quantitative food allergen risk assessment framework could facilitate the promotion of international harmonization of allergen labeling, support food allergic consumers in making safe food choices, and safeguard the health of allergic individuals across various regions and ethnicities. The implementation of food allergen risk assessment could ensure both food supply chain safety and guide the establishment of acceptable allergen cross-contact levels, enhancing food safety and bolstering the integrity and sustainability of the food system.