Duck Tembusu virus (DTMUV) is a neurotropic virus belonging to the genus Flavivirus, and causes massive economic losses to the poultry industry in China and neighbouring countries. Autophagy plays a pivotal role in cellular responses to pathogens and viral pathogenesis. However, little is known about the roles of autophagy in DTMUV replication and virus pathogenesis, especially in neuropathogenesis. In this study, mouse neuroblastoma cells (Neuro-2a) were used to establish a DTMUV infection cell model. Our experiments indicated that DTMUV infection induced incomplete autophagy in Neuro-2a cells. Then, autophagy induced by DTMUV was altered with different autophagy regulators, and we found that incomplete autophagy promoted DTMUV replication. Furthermore, we showed that DTMUV infection activated both the ERK and AMPK pathways, resulting in decreased phosphorylation levels of the autophagy repressor mTOR, subsequently leading to autophagic induction. In addition, we utilized ICR mice as the DTMUV-infected animal model to evaluate the autophagic responses in brain tissues and investigate the effects of autophagy on viral replication and tissue lesions. As a result, we confirmed that DTMUV induced incomplete autophagy in mouse brain tissues and that autophagy inducer treatment promoted DTMUV replication and aggravated DTMUV-induced lesions, whereas autophagy inhibitor treatment led to the opposite effects. Collectively, DTMUV infection induced incomplete autophagy through the ERK/mTOR and AMPK/mTOR signalling pathways to promote viral replication in mouse neuronal cells, and DTMUV-induced incomplete autophagy contributed to the neuropathogenesis of DTMUV.