Candida albicans is the most prominent conditional fungal pathogen, which can cause systemic candidiasis when an individual becomes immunocompromised. The widespread and long-term use of azoles like fluconazole (FLC) has led to a significant increase in drug resistance, posing substantial challenges to clinical treatment. In our previous study, benzyl isothiocyanate (BITC) was extracted from Carica papaya L. seed, and it exhibited a notable inhibitory effect against C. albicans. However, the application of BITC is restricted by its instability, poor water solubility, volatility, and easy degradation. This study aimed to prepare BITC-loaded nanostructured lipid carrier (BITC-NLC) to address these limitations of BITC and enhance antifungal efficacy in vitro and in vivo against C. albicans. The results of physicochemical properties showed that BITC-NLC had small particle size, good physical stability, and high encapsulation efficiency. In vitro, the antifungal effect of BITC-NLC was better than BITC against both sensitive and resistant C. albicans and better than FLC against resistant C. albicans. Moreover, in the in vivo experiment using systemic candidiasis mice model induced by resistant C. albicans, BITC-NLC was more remarkable than BITC and FLC in the increase of the survival rate and the splenic index, the reduction of the fungal burden, and the alleviation of the pathological damage. These findings may be attributed to the enhanced stability and sustained release of BITC. This study highlights the potential of BITC-NLC as a novel and effective formulation for the clinical treatment of drug-resistant C. albicans infections, thereby expanding the application scope of papaya.