The ultramafic-mafic Kharaelakh intrusion in the northwestern part of the Siberian Craton (Russia) hosts major economic platinum-group-element (PGE)-Cu-Ni sulphide deposits. In situ U-Pb, REE and Hf-isotope analyses of zircon from these rocks, combined with detailed study of crystal morphology and internal structure, identify four zircon populations. U-Pb ages of these populations cover a significant time span (from 347 ± 16 to 235.7 ± 6.1 Ma) suggesting multiple magmatic events that cluster around 350 and 250 Ma, being consistent with two recognised stages of active tectonism in the development of the Siberian Craton. The oldest zircon population, however, represents previously unknown stage of magmatic activity in the Noril'sk area. Epsilon-Hf values of +2.3 to +16.3 in the analysed zircons reflect a dominant role of mantle-derived magmas and suggest that juvenile mantle material was the main source for the ultramafic-mafic Kharaelakh intrusion. A significant range in initial 176Hf/177Hf values, found in zircons that cluster around 250 Ma, indicate mixing between mantle and crustal magma sources. Our findings imply that economic intrusions hosting PGE-Cu-Ni deposits of the Noril'sk area have a far more complex geological history than is commonly assumed.