Amphotericin B (AmpB), one of the most commonly used agents in the treatment of severe fungal infections and life-threatening parasitic diseases such as visceral Leishmaniasis, has a negligible oral bioavailability, primarily due to a low solubility and permeability. To develop an oral formulation, medium chain triglycerides and nonionic surfactants in a self-nano-emulsifying drug delivery system (SNEDDS) containing AmpB were combined with room temperature ionic liquids (RTILs) of imidazolium. The presence of ionic liquids significantly enhanced the solubility of AmpB, exhibited a low toxicity and increased the transport of AmpB across Caco-2 cell monolayers. The combination of RTILs with a lipid formulation might be a promising strategy to improve the oral bioavailability of AmpB.