Equine hepacivirus (EqHV), also known as Hepacivirus A, represents the most closely related genetic homologue of human hepatitis C virus (HCV). Although detected worldwide, limited information on the clinical features of this infection is available and on the mechanisms by which EqHV is transmitted. In this study, we describe a spread of infection of EqHV that occurred in a small stable of horses in southern Italy. The RNA of EqHV was detected in 6/13 (46.2%) sera of the horses introduced into the herd, at different times, over a period of approximately one year. Based on the sequencing analyses of genomic portions located in the NS5B, 5′UTR, and NS3 genes, the viruses detected in the animals were genetically highly related (100% nt identity) to each other. The nearly full-length genome of the virus identified from two horses was generated. For one animal with a profile of chronic infection, the genome sequence was determined with a 7-month interval, revealing 26nt changes resulting in 11 nonsynonymous intrahost nucleotide variations. Overall, based on the epidemiological information, we support the hypothesis that horizontal transmission occurred in the herd.