This study investigated the in vitro bioactivities of extracts obtained from viscera, spines, shells, and gonads of Stomopneustes variolaris using subcritical water extraction (SWE) at 110 °C, 150 °C, 190 °C, and 230 °C and Soxhlet extraction. The highest amounts of phenolics (22.68 ± 0.05 mg GAE/g), flavonoids (27.11 ± 0.10 mg RE/g), and proteins (40.25 ± 0.84 mg BSA/g) were recorded from gonads at 230 °C, whereas maximum sugar content (23.38 ± 1.30 mg glucose/g) was in viscera at 150 °C. Gonads at 230 °C exhibited the highest DPPH activity (78.68 ± 0.18%), whereas viscera at 150 °C exhibited the highest ABTS⁺ (98.92 ± 1.27%) and protein denaturation inhibition activity (37.13 ± 9.94%). Viscera at 110 °C claimed the highest amylase inhibition (42.46 ± 0.83%), and spines at 150 °C had the highest anticancer activity (IC₅₀ = 767.47 μg/mL). SWE achieved superior results in bioactive compound recovery and detected higher levels of bioactivities (p < 0.05). Results suggest processing sea urchin extracts via SWE has potential application to the food and pharmaceutical industries.