Acanthamoeba castellanii is an organism that causes Acanthamoeba keratitis, an infectious disease. Acanthamoeba are protists that generally inhabiting soils, freshwater, and sea water, but can also infect the cornea due to dirty water infiltration if contaminated contact lenses are worn. In this study, we focused on four branched medium chain fatty acids-2-ethylhexanoic acid, 3,5,5-trimethylhexanoic acid along with their salts, potassium 2-ethylhexanoate, and potassium 3,5,5-trimethylhexanoate. We examined their antimicrobial effect toward A. castellanii and aimed to search for new drugs to be used in contact lens disinfecting solutions. The minimum inhibitory concentrations (MICs) of 2-ethylhexanoic acid and 3,5,5-trimethylhexanoic acid showed growth reduction of 4-log units (99.99% suppression) in A. castellanii upon 10 min incubation at 12.5 v/v%. In addition, at a diluted concentration of 6.25 v/v%, 2-ethylhexanoic acid produced a 4-log units reduction at 180 min and for 3,5,5-trimethylhexanoic acid, a 4-log units reduction at 60 min. The MICs of potassium 2-ethylhexanoate showed growth reduction of 4 log units in A. castellanii upon 10 min incubation at 2.50 w/v%. However, potassium 3,5,5-trimethylhexanoate showed growth reduction of 4-log units in A. castellanii upon 180 min incubation at 5.00 w/v%. Based on the results of MICs, a verification test of 3,5,5-trimethylhexanoic acid and potassium 2-ethylhexanoate was conducted. As a result, approximately 2.1 logarithmic growths were observed in the control consisting of 10% Tween 80 compared to the initial cell number, and the amoeba growth reduction with 3,5,5-trimethylhexanoic acid could not be confirmed up to a concentration of 0.0122 v/v%. Potassium 2-ethylhexanoate salt was not confirmed to reduce amoeba growth up to 0.625 w/v%. However, the amoeba growth reduction could not be confirmed with the tests where control pH-adjusted solution was applied, either. In the light of the above-mentioned results, it was revealed that 3,5,5-trimethylhexanoic acid exhibits the highest anti-amoeba effect among the four tested branched medium chain fatty acids. This result indicated the possibility to use it in contact lens disinfectant solutions as a novel drug against Acanthamoeba keratitis.