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<i>Cutibacterium acnes</i> is abundant and commonly exists as a superficial bacteria on human skin. Recently, the resistance of <i>C. acnes</i> to antimicrobial agents has become a serious concern, necessitating the development of alternative pharmaceutical products with antimicrobial activity against <i>C. acnes</i>. To address this need, we evaluated the antimicrobial activity of CKR-13—a mutant oligopeptide of FK-13 with increased net charge and theoretical α-helical content—against <i>C. acnes</i> in modified Gifu Anaerobic Medium broth by determining the minimum inhibitory concentration (MIC). CKR-13 exerted greater antimicrobial activity against <i>C. acnes</i> than FK-13 in the broth at pH 7.0. The antimicrobial activity of CKR-13 with RXM against <i>C. albicans</i> was pH-dependent. The ionization of CKR-13 and pH-dependent growth delay of <i>C. albicans</i> was suggested to be associated with the increase in CKR-13 antimicrobial activity.