Five U-Pb CA-ID-TIMS high-precision ages were obtained from single zircon crystals separated from tuffs or ignimbrites embedded in Pennsylvanian to Asselian sediments of the Intra-Sudetic, Krkonoše-Piedmont and the adjacent part of the Mnichovo Hradiště basins. The new radioisotopic data are used for extrapolation of ages of dated lithostratigraphic units. The existing borehole network in the Late Paleozoic continental basins of central and western Bohemia and in the Sudetic area, and similarity of their stratigraphically equivalent strata including some common lacustrine horizons allow a detailed lithostratigraphical correlation between these two areas. This in turn, allows combining our new radioisotopic data with similar high precision U-Pb CA-ID-TIMS ages from basins in central and western Bohemia. Result of this correlation is an integrated time-calibrated lithostratigraphical model for the entire Pilsen–Trutnov Basin Complex. This model shows basin-wide alternation of periods of deposition and prevailing non-depostion/erosion due to tectonic events (phases) related possibly from accumulation of stress at plate boundaries. Combined data prove the existence of two new hiatuses; between (1) Duckmantian and Bolsovian and (2) Cantabrian and Barruelian, which have not been previously recognized from the biostratigraphic record. Existing macrofloral and faunal data from these basins were used to assign the lithostratigraphic units to particular biozones and their correlation. In addition, radioisotopic data allowed calibrating these floral as well as terrestrial/fresh-water faunal biozones and their correlation to global stages and thus contribute to integrated and radioisotopically calibrated marine/non-marine biostratigraphy. Four periods of increased volcanic activity have been recognised. Radioisotopic ages of volcanic rocks intercalated in sediments of the basin fill correspond with similar ages of intrusive magmatic activity and demonstrate the relationship between plutonic and volcanic processes.