The essential oils (EOs) isolated from the fresh aerial parts of Ruta chalepensis L. collected in North Lebanon were obtained by solvent-free microwave extraction (Milestone®), yielding 0.12% EO from both the leaves and a mixture of stems and leaves. The EOs were characterized by GC/MS analysis, and 27 components were identified, which were primarily ketones (88.0–93.2%). The main components were nonan-2-one and undecan-2-one. The antimicrobial activity of the EOs against a Gram-positive and a Gram-negative bacterium, a yeast, and a dermatophyte was evaluated using the broth-microdilution technique and expressed as minimal inhibitory concentration (MIC). The EOs revealed moderate in vitro antifungal activity against Trichophyton rubrum and Candida albicans.