The 2176 Ma peralkaline and agpaitic Nechalacho Layered Suite (NLS) is the youngest and most evolved member of the Paleoproterozoic Blatchford Lake Igneous Complex, which comprises a series of gabbro, granite, quartz syenite and nepheline syenite intrusive rocks that were emplaced within the Slave Craton of Canada. The nepheline–sodalite syenites of the NLS form a laccolithic intrusive body >4 km2 in plan and >1·1 km deep that crops out at Thor Lake, Northwest Territories, in the centre of the complex. Igneous layering is defined by variable proportions of nepheline, sodalite, end-member aegirine and annite, K-feldspar, albite and eudialyte. Two layers in the upper part of the intrusion, the Basal Zone and the Upper Zone, host one of the world’s largest rare earth element (REE) and niobium resources, the Nechalacho Rare Metal Deposit. The principal magmatic REE–Nb-mineral is kentbrooksite (a eudialyte group mineral); fluornatropyrochlore, bastnäsite-(Ce) and fluorbritholite-(Ce) occur in minor proportions. Based on whole-rock and mineral chemistry and phase equilibria for the NLS and cogenetic granitoids, the units of the Blatchford Lake Igneous Complex are considered to have formed by batch melt extraction from a deep crustal magma chamber in which a mantle-derived, heterogeneous mafic parental melt underwent fractional crystallization. The magma that crystallized to form the NLS represents the final and most evolved batch. It was essentially magnesium-free and highly enriched in Zr, REE, Nb, carbon species, fluorine and chlorine. Based on its mineralogy, the NLS crystallized from ∼800 to < 500 °C at a pressure of ∼4 kbar and oxygen fugacity initially below the annite–aegirine equilibrium (QFM + 0·2 to QFM + 1·3 at 500–882 °C, where QFM is the quartz–fayalite–magnetite buffer); fO2 later increased in response to auto-oxidation of the residual melt by annite crystallization. In situ fractional crystallization of the intrusion proceeded both upwards and downwards. Early crystallization of REE–Nb–Zr minerals was inhibited owing to the low melting temperature of eudialyte. The REE, Nb, Zr and volatile species (fluorine, carbon) were enriched in an iron-rich residual melt until the magma became saturated with respect to eudialyte, forming cumulates and layers containing interstitial eudialyte in the upper part of the intrusion. Mineral fractionation during internal crystallization led to large variations in light/heavy REE, Zr/Hf and Nb/Ta, with the Basal Zone recording the strongest heavy REE enrichment.