Epstein-Barr virus (EBV) miRNAs are expression in various human tissues, including the human colon. We have previously shown that the EBV miRNA miR-BART10-3p is higher expressed in colon cancer tissue compared to adjacent normal tissue. Here, we aim to identify and validate novel human targets of miR-BART10-3p. MiR-BART10-3p mimics were transfected into the two colon cancer cell lines, SW620 and LS411N, and changes in RNA expression were evaluated by RNA-seq. Several genes showed significant changes in gene expression upon miR-BART10-3p transfection, and genes that were significantly differentially expressed in both cell lines were more often down-regulated in miR-BART10-3p transfected cells, indicating regulation by miR-BART10-3p. Candidate human targets of miR-BART10-3p were predicted using TargetScan, and two genes with predicted target sites, MAT2B and CCND1, were functionally validated as miR-BART10-3p targets. Together, we here present several novel candidate human targets of miR-BART10-3p, thereby increasing the understanding of miR-BART10-3p in colon cancer.