The increase in antimicrobial resistance poses a significant challenge in medicine, necessitating the exploration of novel antimicrobial agents. Temporin A and Apidaecin B, two naturally occurring antimicrobial peptides (AMPs), have garnered attention for their potent bactericidal properties. This study aimed to investigate the antimicrobial activities of Temporin A and Apidaecin B against clinical strains isolated from blood cultures and evaluate their potential as alternative therapeutic agents. A total of 12 Escherichia coli, 13 Klebsiella pneumoniae, 13 Staphylococcus aureus, and 12 Staphylococcus epidermidis strains were used for antimicrobial susceptibility tests. Antimicrobial activities were evaluated using the broth microdilution method. MIC values were detected as <3.9 for Temporin A against S. aureus and S. epidermidis and 7.81 for Apidaecin B against E. coli. The results underscore the potent antimicrobial properties of Temporin A against S. aureus and S. epidermidis, and Apidaecin B against E. coli. Further research is needed to optimize AMPs’ stability, delivery mechanisms, and efficacy in vivo.