Rye is an underappreciated cereal, despite its high protein content and bioactive compounds, including polyphenols and arabinoxylans. It has been demonstrated that enzymatic hydrolysis of rye protein yields multifunctional hydrolysates with notable radical-scavenging activity and the ability to inhibit ACE and DPP-IV enzymes in vitro. Additionally, the commercial Aspergillus oryzae peptidase preparation known as Flavourzyme is recognized for producing bioactive hydrolysates without undesirable sensory attributes, making such hydrolysates suitable for the development of functional foods. Therefore, the objective of this study was to optimize the enzymatic hydrolysis of a rye protein isolate using Flavourzyme to maximize its antioxidant properties. The rye protein isolate was obtained using a solubilization-precipitation method, and the systems to be hydrolyzed were prepared at 10% (w/v) in phosphate buffer at pH 7.5 and sterilized prior to hydrolysis. A central composite design was used, in which the factors evaluated were hydrolysis time (2, 5, and 8 h) and the enzyme-to-protein ratio (3, 6, and 9%), with temperature and oscillatory agitation held constant at 60 °C and 130 rpm, respectively. Likewise, the output signal to be optimized was antioxidant capacity, measured using the DPPH assay. The optimization process yielded a model with a coefficient of determination (R²) of 0.981, with optimal conditions of a 10.24% enzyme-to-protein ratio and 9.24 h of hydrolysis, achieving an antioxidant activity of 50.12 ± 0.41%, which fell within the confidence interval of the predictive model. The results obtained allow for the establishment of reproducible hydrolysis conditions that can be scaled up to production processes for the development of functional foods or nutraceuticals based on rye protein.