This study aimed to assess the antimicrobial susceptibility testing (AST) using the disc diffusion method of Brucella melitensis isolates (n = 42) recovered from humans and slaughtered seropositive animals to 10 antibiotics commonly prescribed for the treatment of human brucellosis. Additionally, we used ERIC-PCR to evaluate the genetic diversity of Brucella isolates recovered from animals and humans in Upper Egypt and the Egyptian borders. The Brucella isolates from small ruminants (n = 29) and humans (n = 13) with fevers of unknown cause were identified as B. melitensis biovar 3 by both bacteriological and molecular methods. Concerning susceptibility to antibacterial therapeutics, three human isolates (3/13; 23%) and 23 animal isolates (23/29; 79.3%) showed resistance to rifampicin. All B. melitensis strains recovered from small ruminants and six (46%) strains of human origin conferred resistance to sulfamethoxazole-trimethoprim, marking a first record in Egypt. All the isolates were resistant to ciprofloxacin. ERIC-PCR fingerprinted the B. melitensis selected strains into 18 (M1-M18) ERIC types (ET), of which 2 ERIC types consist of 2 identical strains: one ET (M1_Human_Fayoum) for human isolates (2 isolates) and another ET (M8_Goat_Wadi Jadid) for goat isolates (2 isolates). In conclusion, most Egyptian B. melitensis isolates recovered in our study were susceptible to most antibiotics commonly prescribed for human brucellosis treatment. The in vitro resistance of Egyptian B. melitensis strains to sulfamethoxazole-trimethoprim, ciprofloxacin, and rifampicin highlights the necessity of regular antibiotic susceptibility testing and breakpoint updating to minimize human brucellosis relapse cases. The emergence of resistant Brucella strains to various antibiotics recommended by the WHO (first and alternative therapies) will reduce the efficacy of treatment options, potentially leading to further complications. The high genetic diversity of B. melitensis bv3 based on ERIC-PCR fingerprinting patterns demonstrates the simplicity, reliability, and cost-effective genotyping approach for distinguishing between Brucella strains, particularly in developing countries.