The Moldanubian domain of the Variscan Bohemian Massif is characterized by a large number of rare-element pegmatites, which are of possible economic importance. In order to investigate timing relationships between emplacements of Li-bearing rare-element pegmatites and the tectonometamorphic and magmatic evolution of this domain, 10 in situ U–Pb dates of minerals of the columbite–tantalite group from eight rare-element pegmatites, belonging to different pegmatite fields, have been obtained by the LA–SF–ICP–MS technique. As in former studies, our results suggest that assimilation of common Pb is very limited, and diffusion of radiogenic Pb is of minimal importance in columbite. Two ages of emplacement have been obtained. An older episode at ~333 ± 3 Ma follows closely the generalized melting event that occurred at the end of the Moravo–Moldanubian phase, during exhumation of high-pressure rocks. The younger episode, at ~325 ± 4 Ma, seems to have been contemporaneous with the beginning of the Bavarian phase. The emplacement of Li-bearing rare-element pegmatites in the Moldanubian domain is the oldest known magmatic event involving rare-element-enriched melts during the Variscan orogeny. Our results show that the emplacement of Li-bearing rare-element pegmatites is not genetically related with the granulite-facies metamorphism of the lower crust. Rather, the magmas could have originated directly by partial melting linked to the formation of migmatites contemporaneous with the exhumation of high-pressure rocks.