The Ruwai deposit is Indonesia's largest Zn‐Pb‐Ag skarn deposit and is located in Lamandau district, Central Borneo, within the Central Borneo metallogenic belt. This skarn deposit consists of four main zones, namely Gojo, Karim, Ruwai, and Southwest Gossan Zones. The skarn orebodies are mostly hosted by limestone of the Jurassic Ketapang Complex where quartz diorite of the Cretaceous Sukadana Granitoid is the ore‐causative intrusion. Despite the several mineralogical studies carried out in this deposit, there is still a lack of knowledge of its geochemical characteristics. This study evaluates the element mobility during skarn formation on the basis of skarn and ore mineralogy combined with lithogeochemical data of the intrusions, sedimentary wall rocks, and skarn bodies. The skarn mineralogy of the Ruwai skarn complex can be divided into prograde, retrograde and supergene stages. The prograde stage is characterized by the formation of an anhydrous assemblage of garnet‐pyroxene, while the retrograde stage features the replacement of prograde minerals by predominant epidote‐chlorite‐actinolite. The mineralization was first introduced during the late prograde stage, while the formation of massive orebodies attributed to the retrograde stage. The skarn samples show a wide range of major element contents, but both the mineralized skarn and massive orebodies show similar trace and rare‐earth elements patterns in global Phanerozoic limestone‐ and upper crust sedimentary rocks‐normalized spider diagrams. The skarn and orebodies, as well as the metalimestone in this study area, are depleted in REE, although HREE are higher than LREE. Most metals (e.g., Zn, Pb, Ag, Cu, Fe) in skarn and associated orebodies, interpreted to be predominantly magmatic‐sourced, show co‐occurring enrichment or depletion relative to the metalimestone and intrusive rocks. The isocon analysis shows that there was significant mass loss as a consequence of significant volatile loss, such as CO2, during skarn formation. Major oxides and large ion lithophile elements mostly behaved as mobile elements during skarn formation, whereas rare‐earth and high field strength elements tended to be immobile. However, the occurrence of several HFSE‐ and REE‐bearing minerals in Ruwai deposit (i.e., zircon, thorite, cerite, cerianite, monazite, allanite), suggesting minor or local mobility of these elements. Such unexpected behavior can be justified by the occurrence of fluorine‐rich hydrothermal fluid, which could have been responsible for the increasing mobility of these elements.