Brucella species are highly monomorphic, with minimal genetic variation among species, hindering the development of reliable subtyping tools for epidemiologic and phylogenetic analyses. Our objective was to compare two distinct multiple-locus variable-number tandem-repeat analysis (MLVA) subtyping methods on a collection of 101 Brucella melitensis isolates from sporadic human cases of brucellosis in Egypt (n = 83), Qatar (n = 17), and Libya (n = 1). A gel-based MLVA technique, MLVA-15(IGM), was compared to an automated capillary electrophoresis-based method, MLVA-15(NAU), with each MLVA scheme examining a unique set of variable-number tandem repeats. Both the MLVA(IGM) and MLVA(NAU) methods were highly discriminatory, resolving 99 and 101 distinct genotypes, respectively, and were able to largely separate genotypes from Egypt and Qatar. The MLVA-15(NAU) scheme presented higher strain-to-strain diversity in our test population than that observed with the MLVA-15(IGM) assay. Both schemes were able to genetically correlate some strains originating from the same hospital or region within a country. In addition to comparing the genotyping abilities of these two schemes, we also compared the usability, limitations, and advantages of the two MLVA systems and their applications in the epidemiological genotyping of human B. melitensis strains.