In order to alter the solubility and bioavailability of various functional lipids and plant essential oils (EOs), it is possible to prepare their oil in water (O/W) nanoemulsions. Thyme O/W nanoemulsions were prepared under subcritical water conditions (at 120°C and pressure of 1.5 atm for 2 h), using Tween 20, Tween 80, saponin, Arabic gum, xanthan gum, and sodium caseinate as emulsifiers. Results indicated that nanoemulsions with minimum mean droplet size of 11.5 and 12.6 nm were produced using Tween 20 and 80, respectively. Moreover, nanoemulsions with minimum polydispersity index (0.139) and maximum mean value of zeta potential (−24.5 mV) were provided utilizing xanthan gum and saponin, respectively. Results also revealed that the prepared nanoemulsions using saponin had maximum antioxidant activity based on percentage of scavenging ability (40.6%) and bactericidal effects against Streptococcus mutans as manifested in the formed clear zone (diameter of 21 mm). Morphological assessment of all the prepared nanoemulsions demonstrated that spherical thyme nanodroplets were formed in the colloidal solutions which revealed that all the prepared nanoemulsions had high thermodynamic stability due to the minimum surface energy level of the formed nanodroplets. This can increase applications of the prepared thyme O/W nanoemulsions in the aqueous food and pharmaceutical formulations.