<i>Candida albicans</i> is a major cause of fungal diseases in humans, and its resistance to available drugs is of concern. In an attempt to identify novel antifungal agents, we initiated a small-scale screening of a library of 199 natural plant compounds (i.e., natural products [NPs]). <i>In vitro</i> susceptibility profiling experiments identified 33 NPs with activity against <i>C. albicans</i> (MIC ₅₀ s ≤ 32 μg/ml). Among the selected NPs, the sterol alkaloid tomatidine was further investigated. Tomatidine originates from the tomato ( <i>Solanum lycopersicum</i> ) and exhibited high levels of fungistatic activity against <i>Candida</i> species (MIC ₅₀ s ≤ 1 μg/ml) but no cytotoxicity against mammalian cells. Genome-wide transcriptional analysis of tomatidine-treated <i>C. albicans</i> cells revealed a major alteration (upregulation) in the expression of ergosterol genes, suggesting that the ergosterol pathway is targeted by this NP. Consistent with this transcriptional response, analysis of the sterol content of tomatidine-treated cells showed not only inhibition of Erg6 (C-24 sterol methyltransferase) activity but also of Erg4 (C-24 sterol reductase) activity. A forward genetic approach in <i>Saccharomyces cerevisiae</i> coupled with whole-genome sequencing identified 2 nonsynonymous mutations in <i>ERG6</i> (amino acids D249G and G132D) responsible for tomatidine resistance. Our results therefore unambiguously identified Erg6, a C-24 sterol methyltransferase absent in mammals, to be the main direct target of tomatidine. We tested the <i>in vivo</i> efficacy of tomatidine in a mouse model of <i>C. albicans</i> systemic infection. Treatment with a nanocrystal pharmacological formulation successfully decreased the fungal burden in infected kidneys compared to the fungal burden achieved by the use of placebo and thus confirmed the potential of tomatidine as a therapeutic agent.