The outcome of viral pathogenesis is determined by many biological components including small non-coding microRNAs (miRNAs). Studies have shown that miRNA binding to complementary transcript sequences alter the gene expression of host factors and subsequently impact the host-virus interaction. However, most experiments implicating miRNAs in viral pathogenesis are done ex vivo and/or using viruses which are not natural pathogens of hosts. Here, to investigate the in vivo role of miRNAs in natural host-virus association, the Drosophila melanogaster-Drosophila C virus (DCV) model system was used. D. melanogaster infection with the +ssRNA virus DCV induced differential abundance in miRNA levels, with the largest change observed for miR-956-3p. Loss of miR-956 in miR-956 knockout flies resulted to delayed viral accumulation and virus-induced mortality compared to wild-type flies, demonstrating that the observed decrease in miR-956 during virus infection has antiviral and host-protective consequences. miR-956 putative targets were identified and 84 of the targets were assayed for regulation upon miR-956 loss-of-function (LOF) and DCV infection. The virus-stimulated gene (VSG) Ectoderm-expressed 4 (Ect4) showed up-regulation upon miR-956 LOF and down-regulation upon DCV infection, suggesting miR-956 negative regulation of Ect4 during viral infection. To analyse the role of Ect4 regulation during DCV infection, Ect4 knockdown flies were challenged with DCV. Inverse to the effects of miR-956 suppression, decrease in Ect4 accelerated virus accumulation and virus-induced mortality. Take together, results show that, in vivo, the antiviral and host-protective consequences of miR-956 regulation during infection of the model D. melanogaster with its natural pathogen DCV is exerted through miR-956 modulation of the VSG Ect4.