The aim of this study was to elucidate in vitro antiamoebic activity of antimicrobial agents at short exposure times similar to those used for actual treatment against Acanthamoeba strains isolated from patients with keratitis. The 5 clinical Acanthamoeba isolated in Japan were used in this study. Identification of genotypes for the Acanthamoeba isolates was performed using partial 18S ribosomal DNA (rDNA), including the ASA.S1 region sequences. Fluconazole, miconazole, itraconazole, voriconazole, amphotericin B, natamycin (pimaricin), and micafungin (antifungal agents), and chlorhexidine (a biguanide disinfectant), and sulfamethoxazole and paromomycin (antibacterial agents) were used to determine the antiamoebic activity against Acanthamoeba, which were determined by 50% and 90% growth inhibitory concentrations (IC50 and IC90) following exposing to each drug at 25°C for 7 days and 12 h. Among the tested antimicrobial agents, natamycin strongly inhibited the growth of all Acanthamoeba isolates at low concentration in both the 7-day (IC90 = 4.1 μg/mL) and 12-h (IC90 = 11.6 μg/mL) assays. Additionally, sulfamethoxazole exhibited strong antiamoebic activity (IC90 = 9.8 μg/mL) at low concentration in the 7-day assay. Our findings showed that natamycin ophthalmic solution might be an effective agent against Acanthamoeba keratitis. Additionally, frequent administration of sulfamethoxazole ophthalmic solution or systemic sulfamethoxazole-trimethoprim is also considered as an effective treatment for Acanthamoeba keratitis.