Plant viral diseases are incurable and reduce fruit yield and quality, causing economic losses. Damages vary depending on the virus-host combination, virulence, and cultivar susceptibility. Therefore, the fundamental way to prevent virus damage is to cultivate virus-free plants. Thermotherapy, cold therapy, chemotherapy and cryotherapy combined with microshoot tip culture are used to eliminate fruit tree viruses. This review describes fruit viral diseases and summarizes the current elimination methods. Next-generation sequencing (NGS) has also been used to identify and diagnosis new fruit crop viruses. Therefore, studies are needed to optimize elimination methods for NGS-identified viruses.