Syzygium aqueum, consisting of various fruit colors, is one of the plants that have been used as traditional medicine. This study aims to evaluate and compare phytochemical, antioxidant, and cytotoxic activities and total phenolic content of leaves and stem bark extracts of S. aqueum with pink and red fruits, in order to identify the best extract that can be used as a natural antioxidant. Phytochemical constituents were evaluated qualitatively using chemicals, while cytotoxic activities were identified using the brine shrimp lethality test. Total phenolic content was determined via the Folin–Ciocalteu method. Leaves and stem bark of S. aqueum contained flavonoids, phenolics, and triterpenoids, but the stem bark also contained saponins and alkaloids. Methanol and ethyl acetate extracts of leaves and stem bark were categorized as very powerful antioxidants to DPPH (IC50 9.71–38.69 μg/mL) and hydrogen peroxide (IC50 16.44–44.02 μg/mL), while hexane extracts were inactive. Methanol, ethyl acetate, and hexane extracts of leaves and stem bark were categorized as moderately cytotoxic to A. salina larvae (LC50 104.04–440.65 μg/mL). Comparing leaves and stem barks, antioxidant and cytotoxic activities of stem bark extracts were higher than those of leaves extracts. Total phenolic content of leaves extracts was higher than that of stem bark extracts where the order of total phenolic content progressed from methanol extracts > ethyl acetate extracts > hexane extracts. Therefore, the stem bark of S. aqueum was identified as the better source of natural antioxidant compared with the leaves.