In this study, a safety evaluation was conducted to confirm if the Enterococcus faecium CKDB003 strain obtained by selection from a mixed fermentation of fruit and milk is suitable for use as a probiotic. The MIC value for the 10 antibiotics specified in the EFSA guidance was below the acceptable cut-off value. The antibiotic resistance genes aac(6')-li, eatAv, and msr(C) exist by whole genome sequencing, but are in the chromosome and not in the plasmid, thus confirming that there is no possibility of transmission to other microorganisms. It was confirmed that cytolysin (cylA, cylB, cylI, cylL-l, cylL-s, cylM, cylR1, cylR2), aggregation substance (asa1, asp1), collagen adhesion (ace), enterococcal surface protein (esp), endocarditis antigen (efaA), hyaluronidase (hyl) and gelatinase (gelE) were not present in the genome by examining the genes of factors related to virulence. Also, the biochemical analysis showed no toxic enzyme activities, and no virulence genes were detected by the PCR method. Thus, the E. faecium CKDB003 strain can be safely used as a health functional food probiotic, based on the results of the safety assessment.