Protein hydrolysates have been reported to possess numerous bioactivities. However, research on melon (Cucumis melo L.) seed protein (MSP) hydrolysate is limited. This study aimed to analyze the antioxidant and hypocholesterolemic properties of MSP hydrolysate. Protein from melon seed was obtained by conventional alkaline extraction-isoelectric precipitation method. Enzymatic hydrolysis of MSP was carried out using three different proteases: pepsin, thermolysin, and trypsin, with the enzyme-to-substrate (E/S) ratio of 1:50 (w/w). The results showed that all hydrolysates exhibited antioxidant and hypocholesterolemic activity. The thermolysin-digested hydrolysate had significantly greater (p < 0.05) radical scavenging properties, while trypsin produced the highest (p < 0.05) metal ion chelating activity. At 2 mg/mL, thermolysin-derived MSP hydrolysate showed no significant difference (p > 0.05) in HMGR inhibition activity compared to pravastatin. Additionally, the thermolysin hydrolysate had significantly higher (p < 0.05) bile acid binding ability than other hydrolysates. Overall, the MSP hydrolysate produced by thermolysin exhibited stronger antioxidant and hypocholesterolemic activities when compared to those produced by pepsin and trypsin, suggesting its potential effectiveness in nutraceutical applications.