This work explores two methods to encapsulate Thymoquinone (TQ) into lipid nanocapsules (LNCs) for oral administration. TQ was added during the phase inversion temperature method (TQ-LNCs-1) or to unload LNCs dispersion (TQ-LNCs-2). LNCs were evaluated for mean diameter, polydispersity index (PDI), ζ-potential, drug loading (DL), drop tensiometer, storage stability, in vitro stability in simulated gastrointestinal fluids (SGIF), and intestinal permeability across Caco-2 cells. TQ-LNCs-1 and TQ-LNCs-2 produced NPs (58.3 ± 3.7 nm and 61.5 ± 3.5 nm, respectively), with a DL of 8.7 ± 0.2 and 7.7 ± 0.6 mg/mL of suspension, respectively. For both, less than 14% of TQ was released in SGIF, and a minor increase in TQ intestinal permeability with LNCs compared to free TQ was observed. TQ-LNCs represented a promising formulation for oral delivery of TQ. Encapsulation of TQ by adding it at LNCs dispersion can be extended for further drugs.