(1) Background: Thymus vulgaris L. (thyme) essential oil (TEO) has gained much attention because of its long history of medicinal usage. However, the lack of precise chemical profiling of the TEO and methods to optimize the bioactivity and delivery of its constituents has hampered its research on quality control and biological function; (2) Methods: The current study aimed to analyze the TEO’s chemical composition using the GC-MS method and identify its key components. Another objective of this work is to study the impact of the protective layer of amphiphilic oligochitosan (AOC) on the physicochemical stability and transdermal potentials of TEO multilayer nanoemulsions formulated by the incorporation of TEO, Tween80, lecithin (Lec), and AOC; (3) Results: The AOC protective layer significantly improved the stability of TEO-based NEs as revealed by the constancy of their physicochemical properties (particle size and zeta potential) during storage for a week. Excessive fine-tuning of thyme extract NEs and the AOC protective layer’s persistent positive charge have been contributed to the thyme extract’s improved anti-inflammatory, transdermal, and anti-melanoma potentials; (4) Conclusions: the AOC-coated NEs could offer novel multifunctional nanoplatforms for effective transdermal delivery of lipophilic bioactive materials.