Thymoquinone is the main bioactive component of the plant Nigella sativa, which is commonly known as black seeds and has several therapeutic effects. However, clinical applications of thymoquinone are limited due to its hydrophobic nature. In this study, thymoquinone is encapsulated in albumin nanoparticles by using a microfluidic platform to overcome this limitation. The mean particle sizes of empty and thymoquinone-loaded nanoparticles are determined as 271.3 and 315.6 nm, respectively, with polydispersity index values both lower than 0.25. In addition to particle size distribution measurements, characterizations of the prepared nanoparticles such as zeta potential measurements, in vitro release studies, as well as scanning electron microscopy, Fourier-transform infrared, and differential scanning calorimetry analyses are also carried out. To determine the effect of thymoquinone on neural regeneration, planarians are used as the model organism. After application of free and encapsulated thymoquinone, planarians are amputated and the fragments are observed in terms of head and tail regeneration, swimming pattern, and behavior. The results indicate that thymoquinone affects their behavior and primarily enhances head regeneration of planarians. In addition, it is shown that encapsulation of thymoquinone not only enhances the thermal stability of the molecule but also decreases its toxicity.