Black cumin (Nigella sativa) is an important medicinal plant in the pharmacological industry. It is cultivated on a commercial scale, but its seeds have a slow, unsynchronized germination rate. Enhancing seed germination is crucial for improving the production of black cumin. The influence of presowing treatments [gibberellic acid (GA3), potassium nitrate, salicylic acid, and stratification at 4 °C] on seed germination was assessed. Seed germination was determined daily for 30 days, and germination parameters, including final germination percentage (FGP), corrected germination rate, number of days to reach 50% of FGP, and seedling length vigor index, were evaluated. Endogenous contents of GA3 and abscisic acid (ABA) in nonstratified and stratified seeds were estimated using high-performance liquid chromatography (HPLC) and seedling growth was determined in 45-day-old seedlings. All presowing treatments tended to boost early germination for the first 10 days compared with the control. Low concentrations of GA3 at 0.25 g·L−1 also increased FGP (80%) compared with the control group (65.55%). Stratification for 4 weeks provided the greatest FGP value at 95.56%, and stratification for 3 weeks proved to be the most effective treatment for optimal seedling growth. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis patterns of stratified seeds revealed the alteration in intensities of 13 bands and the appearance of a new band (180 kDa) indicating a change in the synthesis of proteins during stratification. Moreover, stratification modulated the endogenous GA3 and ABA contents of black cumin seeds, which alleviated the physiological dormancy and resulted in high and synchronized seed germination.