The axinite-bearing Gukjeon Pb–Zn deposit is hosted by the limestone, a member of the Jeonggaksan Formation, which, in turn, forms the part of the Jusasan subgroup of the Yucheon Group in the Gyeongsang Basin in the southeastern part of the Korean Peninsula. In this study, we attempted to interpret the spatial and temporal relationships among geologic events, including the mineralization of this deposit. We constructed a new 3D orebody model and suggested a relationship between skarn alteration and related mineralization. Mineralization timing was constrained using SHRIMP zircon age dating results combined with boron geochemistry on coeval intrusive rocks. Skarn alterations are restrictively found in several horizons of the limestone formation. The major skarn minerals are garnet (grossular), pyroxene (hedenbergite), amphibole (actinolite and ferro-actinolite), axinite (tizenite and ferro-axinite), and epidote (clinozoisite and epidote). The three stages of pre-skarn, syn-skarn, and post-skarn alteration are recognized within the deposit. The syn-skarn alteration is characterized by prograde metasomatic pyroxene and garnet, and the retrograde metasomatic amphibole, axinite, and epidote. Major skarn sulfide minerals are sphalerite, chalcopyrite, galena, and pyrite, which were predominantly precipitated during the retrograde stage and formed amphibole and axinite skarns. The skarn orebodies seem to be disc- or flat-shaped with a convex form at the central part of the orebodies. The vertical ascending and horizontal infiltration of boron-rich hydrothermal fluid probably controlled the geometry of the orebodies. Considering the whole-rock major, trace, and boron geochemical and geochronological results, the timing of Pb–Zn mineralization can be tightly constrained between the emplacement of boron-poor intrusion (fine-grained granodiorite, 82.8 Ma) and boron-rich intrusion (porphyritic andesite in Beomdori andesitic rocks, 83.8 Ma) in a back-arc basin setting. The boron for mineralization was sourced from late Cretaceous (Campanian), subduction-related magmatic rocks along the margin of the Pacific plate.