The tectonic evolution of terranes and microblocks is crucial for understanding the supercontinental cycle. Sri Lanka, centrally located between East and West Gondwana, offers insights into late Neoproterozoic continental tectonics. Ambiguities in defining boundaries between the Highland Complex (HC) and Wanni Complex (WC) of Sri Lanka prompted this study. Utilising whole-rock major and trace element geochemistry, and U–Pb zircon geochronology, we explore charnockites at the inferred HC-WC boundary, revealing their tectonic nature. Charnockites on the WC side (CWCs) display tholeiitic trends, characterised as Fe-rich, metaluminous A2-type granites. Tectonic discrimination diagrams position CWCs in the within-plate granite field. The 238U/206Pb zircon geochronology of three WC-side charnockites gave Late Neoproterozoic metamorphic ages from 576 ± 37 to 561 ± 50 Ma and middle to early Neoproterozoic protolith crystallisation ages from 1011 ± 46 to 690 ± 15 Ma. Hence, protoliths of CWCs suggest some form of extensional tectonics in a continental environment during the early to middle Neoproterozoic that played a major role in the crustal evolution of the northeastern part of the WC. Out of the collected seven charnockites in the HC side (CHCs), three samples shared geochemical signatures resembling the CWCs. The 206Pb/238U zircon ages of one of the samples yielded crystallisation age of ~780 ± 6 Ma and, metamorphic ages from 608 ± 9 to 541 ± 16 Ma, respectively. The rest of the CHCs exhibit calc-alkaline trend, identified as Mg-rich, metaluminous, I-type granites. Tectonic discrimination diagrams reveal volcanic arc signatures, indicating a subduction-related collisional tectonic setting. Geochemical and geochronological findings, coupled with field relations and prior research, lead to the interpretation that charnockites in the northeastern HC-WC boundary possess a distinctive geodynamic history, implying involvement in two distinct tectonic settings. Presently, at the erosion surface, the north-eastern portion of the HC-WC boundary, exhibits a highly diffused nature and manifests as a mixed rock zone.