The invention relates to topical formulations and methods of use of flucytosine which demonstrate a clear advantage over currently available therapeutic regimens for the treatment and maintenance of fungal infections, particularly vulvovaginal candidiasis. The invention provides compositions which solve the long-standing need for antimicrobial agents which treat effectively resistant strains of Candida spp., especially C. albicans, C. glabrata, and C. tropicalis, and which pose limited risk of side effects, adverse reactions, or the development of resistant pathogens. The invention provides novel topical formulations of flucytosine designed to allow the active drug to act at the local application area, but which inhibit or moderate transdermal or transmucosal absorption of the drug, thus limiting systemic exposure.