The development of selective antifungal agents is crucial to improve therapeutic options while minimizing side effects. This study assessed the potential antimicrobial efficacy of ionic liquids, particularly against fungal pathogens. For this, a functionalized chiral ionic liquid (FCIL) with a naturally occurring (1R,2S,5R)-(−)-menthol moiety and a long alkyl chain was synthesized and characterized using spectral and thermal methods. The antifungal potential of this FCIL was evaluated by examining interactions with artificial fungal and mammalian membranes modeled as Langmuir monolayers. Thermodynamic analyses, complemented by adsorption and penetration experiments, Brewster angle microscopy, polarization modulation infrared reflection absorption spectroscopy, and molecular dynamics simulations, showed that FCIL incorporated into membranes and caused fungal membrane disintegration. This can be related to π-π interactions with ergosterol, a primary fungal membrane sterol, and favorable assimilation into membranes containing dioleoylphosphatidylcholine, an unsaturated phospholipid abundant in fungal cells. Conversely, interactions with mammalian membranes modeled using dipalmitoylphosphatidylcholine and cholesterol were thermodynamically unfavorable due to their tighter packing. These findings underline the FCIL's ability to selectively disrupt fungal membranes and suggest its potential use as a targeted antifungal agent with reduced mammalian cell toxicity. This research highlights the benefit of integrating experimental and computational methods to understand the molecular mechanics driving selective antifungal activity.