The Karaçayır carbonatite is located within the northeastern edge of the Central Anatolian Crystalline Complex, and represents one of the significant rare earth element (REE) mineralizations in Turkey. The carbonatite intrudes the associated syenite as dikes and veins, and is mainly composed of medium- to coarse-grained calcite, and lesser amounts of apatite, mica, amphibole, pyroxene, and magnetite. This study reports new and combined geochemical, radiogenic (Sr, Pb), stable (O and C), and for the first time B and Nd isotopic ratios and in-situ U-Pb age data from the Karaçayır carbonatite. The carbonate separates from the Karaçayır carbonatite are characterized by high Ba (30 to 484 ppm), Sr (613 to 9106 ppm) and total rare earth element (TREE) concentrations (172 to 2892 ppm), which are consistent with geochemical signatures for mantle-derived carbonate melts. The combined δ18OV-SMOW (+10.7 to +19.0 ‰), δ13CV-PDB (−2.9 to +1.8 ‰) and δ11B (−13.9 to −2.9 ‰) data for a majority of the carbonate separates investigated here in contrast indicate that they are the result of open system behavior involving contamination by the country rock (marble), and/or sub-solidus, low temperature alteration. Based on the combined stable and radiogenic isotopic signatures for the least altered/contaminated samples, the carbonatite magma at Karaçayır most likely represents a low-degree partial melt of an isotopically heterogeneous (metasomatized) mantle source containing EM (enriched mantle)-like components and recycled crustal carbon; the latter finding is consistent with those recorded for young (<300 Ma old) carbonatites worldwide. A weighted mean 206Pb/238U age of 69.3 ± 1.7 Ma is obtained for apatite from the Karaçayır carbonatite, and indicates its emplacement within a post-collisional tectonic setting during the late Cretaceous.