Discordant U–Pb data of zircon are commonly attributed to Pb loss from domains with variable degree of radiation damage that resulted from α-decay of U and Th, which often complicates the correct age interpretation of the sample. Here we present U–Pb zircon data from 23 samples of ca. 1.7–1.9 Ga granitoid rocks in and around the Siljan impact structure in central Sweden. Our results show that zircon from rocks within the structure that form an uplifted central plateau lost significantly less radiogenic Pb compared to zircon grains in rocks outside the plateau. We hypothesize that zircon in rocks within the central plateau remained crystalline through continuous annealing of crystal structure damages induced from decay of U and Th until uplifted to the surface by the impact event ca. 380 Ma ago. In contrast, zircon grains distal to the impact have accumulated radiation damage at shallow and cool conditions since at least 1.26 Ga, making them vulnerable to fluid-induced Pb-loss. Our data are consistent with studies on alpha recoil and fission tracks, showing that annealing in zircon occurs at temperatures as low as 200–250 °C. Zircon grains from these samples are texturally simple, i.e., neither xenocrysts nor metamorphic overgrowths have been observed. Therefore, the lower intercepts obtained from regression of variably discordant zircon data are more likely recording the age of fluid-assisted Pb-loss from radiation-damaged zircon at shallow levels rather than linked to regional magmatic or tectonic events.