The Bohemian Massif hosts significant hydrothermal U-deposits associated with shear zones in the high-grade metamorphic basement. But there is a lack of evidence of a genetic link between mineralization and U-fertile igneous rocks. This contribution provides constraints on the major U source of the vein-type U-deposits, the timing of ore formation and the metallogenetic model. The anomalous trace element signatures of the low-temperature hydrothermal deposits (high Zr, Y, Nb, Ti, ∑REE) and their close spatial relation with ultrapotassic rocks of the durbachite series point to a HFSE and REE enriched source rock. The durbachites have high U content (13.4–21.5 ppm) mainly stored in magmatic uraninite and other refractory minerals (e.g., thorite, zircon, allanite) that became metamict over a time interval sufficient to release U from their crystal structure, as suggested by the time gap between emplacement of the durbachites (EMP uraninite U–Pb age ~ 338 Ma) and hydrothermal activity (SIMS uranium ore U–Pb age ~ 270 Ma). Airborne radiometric data show highly variable Th/U ratios (1.5–6.0), likely reflecting a combination between (1) crystallization of magmatic uraninite, (2) hydrothermal alteration, and (3) leaching and mobilization of U along NW–SE-trending fault zones, manifested by elevated Th/U values in the radiometric map. The presence of rare magmatic uraninite in durbachites suggests almost complete uraninite dissolution; EMP imaging coupled with LA-ICP-MS analyses of refractory accessory phases revealed extensive mobilization of U together with HFSE and REE, providing direct evidence for metal leaching via fluid-driven alteration of radiation-damaged U-rich minerals. The large-scale HFSE and REE mobilization, demonstrated by the unusual trace element signatures of the U-deposits, was likely caused by low-temperature (270–300 °C), highly alkaline aqueous solutions containing F-, P-, and K-dominated complexing ligands. The first SIMS U–Pb age of 270.8 ± 7.5 Ma obtained so far for U-mineralization from the Bohemian Massif revealed a main Permian U mineralizing event, related to crustal extension, exhumation of the crystalline basement, and basin formation, as recorded by U–Pb apatite dates (280–290 Ma) and AFT thermal history models of the durbachites. The Permo-Carboniferous sedimentary cover probably represented a source of oxidized basinal brines infiltrating the basement-hosted durbachite plutons and triggering massive metal leaching. The interaction between basin-derived brines and durbachites resulted in significant modification of the chemical composition of the hydrothermal system (K and F release during biotite chloritization, P liberation through monazite alteration), leading to the formation of ore-bearing fluids responsible for the metallogenesis of the basement-hosted unconformity-related U-deposits in shear zones in the Bohemian Massif.