Only some carbonatite–syenite complexes in the world could form carbonatite-related rare earth element (REE) deposits, which is regarded as the main REE origin. The Miocene Dunkeldik carbonatite–syenite complex is located in the Dunkeldik magmatic field in Tajikistan between the Pamir and Tibetan plateaus. So far, the origin, tectonic setting, and REE mineralization potential of the Dunkeldik carbonatite–syenite complex remain unclear due to the limited isotopic values, which inhibit the further understanding the genesis of such carbonatite complex. This study presents zircon U–Pb age, whole-rock geochemical, and Sr–Nd–Pb isotope, and zircon Hf–O isotope data for the Dunkeldik carbonatite–syenite complex on the Pamir Plateau. Zircon U–Pb dating of syenite yielded two concordant ages of 10.27 ± 0.16 and 10.48 ± 0.21 Ma, indicative of formation in a post-collisional extensional setting related to India–Asia collision. Both the carbonatite and syenite exhibit similar enrichments in large-ion lithophile elements (e.g., Sr and Ba) and light REEs, depletions in high-field-strength elements (e.g., Nb and Ta) and heavy REEs, and small Eu anomalies. Whole-rock Sr–Nd–Pb isotopic compositions are highly enriched, with high (87Sr/86Sr)i (0.70971 to 0.70979), low εNd(t) (–8.9 to –9.2), and radiogenic Pb isotope composition (206Pb/204Pb (18.322–18.358), 207Pb/204Pb (15.689–15.695), and 208Pb/204Pb (39.091–39.149)). Zircons Hf-O isotope analyses yield low εHf(t) values (–9.5 to –19.0) and high δ18O value (7.4 ‰–9.5 ‰), respectively. These geochemical and isotopic features indicate that the complex was formed by partial melting of enriched lithospheric mantle during the Miocene India–Asia collision and was assimilated by upper crustal material during magma ascent. The carbonatite and syenite in the complex formed by melt immiscibility. The involvement of crustal material in the magma and less development of fenitization may responsible for the limited REE mineralization potential as compared with other large REE deposits that formed during coeval India–Asia collision.