Ginkgo biloba L. is an ancient plant relic, which is known as a “living fossil”, and is widely cultivated in China. This plant with medical potential and health benefits has drawn the attention of researchers. Ginkgo seeds are rich in protein. Ginkgo seed proteins (GSPs) have good functional properties over many other seed proteins, which have the potential to be utilized as food ingredients. Moreover, GSP contains no restricted amino acids and is easy to be separated. Several GSP isolate with various bioactivities, such as antimicrobial and antioxidative activities, have been purified and evaluated for their bioactive potential. In this review, the separation methods and bioactivities of GSP were summarized, physicochemical characteristics and functional properties were comprehensively reviewed and compared with other seed proteins. Some food applications of GSP were also briefly introduced. Besides, some suggestions and prospects were discussed in this review.