Naegleria fowleri, known as the brain-eating amoeba, is the pathogen parasite that causes primary amoebic meningoencephalitis. None of the currently available therapies are fully effective, mainly due to the inefficacy of pharmacotherapy. In this regard, natural products and related compounds represent a promising strategy for amoebicidal drug discovery. Herein, a series of eight monoterpene phenol derivatives of thymol bearing ester, carbonate, or carbamate moieties were prepared, and screened as potential amoebicidal agents on N. fowleri. The cytotoxicity of these compounds on murine macrophages cell line J774 was also evaluated to assess their selectivity. Compounds 3, 4, 7 and 8 showed significant activity against the N. fowleri trophozoite. Moreover, 4-nitrophenyl thymyl carbonate 8 displayed the highest potency, showing IC50 values of 22.87 and 25.16 μM against N. fowleri trophozoite and cyst stages, respectively, coupled with low cytotoxicity on a mammal cell line. Furthermore, mechanism of action studies revealed that derivative 8 triggered programmed cell death via cytosolic calcium accumulation, mitochondrial alteration, membrane damage, chromatin condensation, and ROS accumulation. In addition, the in-silico ADME analysis indicated that derivative 8 exhibits exceptional drug-likeness meeting all the pharmacokinetic criteria. These results highlight derivative 8 as a promising amoebicidal agent to develop new drugs for the treatment of Naegleria infections.