Medicinal plants produce secondary metabolites with special biological activities, which may be used as new therapeutic alternatives. For instance, tea tree essential oil (TTO) was shown to exert antimicrobial, antifungal, anthelmintic, antiviral, anti-tumor and anti-inflammatory activities. Due to their thermal instability, active principles can be easily degraded by physicochemical processes; therefore, they must be protected to increase their time of action and improve their controlled release. The aim of this review is to discuss formulations incorporating encapsulated TTO as the active ingredient. Micro and nanoencapsulated systems proved to be more thermostable than TTO and to exert better antimicrobial, antifungal, antiparasitic and larvicidal effects. Nanoencapsulation also reduced oil toxicity. Emulsified and hybrid systems developed by various methods showed improved repellent, antibacterial, antifungal and anti-inflammatory activities, thereby proving promising for the pharmaceutical industry. Liposomal formulations produced by hydration of lipid films exhibited constant rate of terpinen-4-ol release. In addition, their incorporation into biomaterials, such as sponges, nanofibers and films, showed great potential for treating infections. Mainly due to the advantages of their incorporation into new drug delivery systems over conventional formulations, there is an interest in the development of systems containing TTO as a pharmaceutical ingredient of plant origin.