Abstract The Ruwai skarn deposit is the largest polymetallic skarn deposit in Borneo and is located in the Schwaner Mountains. The skarns and massive orebodies are hosted in marble of the Jurassic Ketapang Complex, which was intruded by Cretaceous Sukadana granitoids. The prograde-stage garnet and retrograde-stage titanite yielded U-Pb ages of 97.0 ± 1.8 to 94.2 ± 10.3 Ma and 96.0 ± 2.9 to 95.0 ± 2.0 Ma, respectively. These ages are similar to Re-Os ages obtained on sulfides (96.0 ± 2.3 Ma) and magnetite (99.3 ± 3.6 Ma). The U-Pb zircon ages reveal that magmatism at Ruwai occurred in three phases, including the Early Cretaceous (ca. 145.7 and 106.7–105.7 Ma; andesite-dacite), Late Cretaceous (ca. 99.7–97.1 Ma; diorite-granodiorite), and late Miocene (ca. 10.94–9.51 Ma; diorite-dolerite). Based on geochemical and stable isotopic data (C-O-S) the Ruwai skarn ores are interpreted to have formed from oxidized fluids at ca. 160 to 670°C. The ore-forming fluids and metals were mostly magmatic in origin but with significant crustal input. Ruwai skarn mineralization occurred in the Late Cretaceous, associated with Paleo-Pacific subduction beneath Sundaland after the Southwest Borneo accretion. Ruwai is the first occurrence of Cretaceous mineralization recognized in the Central Borneo metallogenic belt.