Ebola virus (EBOV) causes Ebola virus disease (EVD), a severe hemorrhagic fever that has high case fatality rates (CFR). Although previous Ebola miRNA research has mainly focused on host miRNA expression during infection, it has been shown that the Ebola virus also encodes miRNAs. However, further studies are required to fully understand the role of EBOV-encoded miRNAs in infection and pathogenic mechanisms. This study aimed to identify known and novel EBOV-encoded miRNAs and predict their potential functions in Ebola virus pathogenic mechanisms. Previously available, small RNASeq data was reanalyzed to identify the miRNAs and predict their cellular targets and potential functions. Four EBOV-encoded miRNAs, EBOV-mir-M1 (4390-4414), EBOV-mir-M4 (11501-11523), EBOV-mir-M2 (8288-8309), and EBOV-mir-M3 (9885-9906) were identified and expressed specifically in the Ebola-infected human adult retinal pigment epithelial (ARPE) cells. EBOV-mir-M1 (4390-4414) was expressed up to 19-fold higher than the other three miRNAs. The miRNAs identified were predicted to target genes associated with several pathways, including calcium signaling, MAPK signaling, tight junction pathway, necroptosis, cytosolic DNA sensing, type I interferon signaling, and cytokine-mediated signaling. These pathways are known to play critical roles in Ebola infection and pathogenic processes. This study contributes to elucidating the role of Ebola virus-encoded miRNAs in infection and pathogenesis. It demonstrates the expression of EBOV-encoded miRNAs with potential functions in human ARPE cells, providing a better understanding of the mechanisms underlying Ebola virus infection.