The Ikole–Itapaji Basement Complex of southwestern Nigeria is part of the Precambrian Nigerian Basement Complex and possesses considerable potential for structurally controlled metallic mineralization. This study integrated high-resolution aeromagnetic data with trace element geochemistry to delineate mineralization zones and identify prospective exploration targets. Twenty representative rock samples were analyzed for trace elements using Inductively Coupled Plasma–Mass Spectrometry (ICP–MS) following partial multi-acid digestion (HCl, HNO₃, and HClO₄) combined with lithium metaborate fusion to ensure complete dissolution of refractory silicate minerals and accurate trace element determination. High-resolution aeromagnetic datasets were processed using Total Magnetic Intensity (TMI), Reduction-to-Equator (RTE), First Vertical Derivative (FVD), Analytical Signal (AS), Euler Deconvolution, and lineament density analyses. Pearson correlation and factor analyses were employed to evaluate elemental associations and mineralization controls. The aeromagnetic results revealed dominant NE–SW, NW–SE, and E–W structural trends comprising faults, fractures, and shear zones that controlled hydrothermal fluid migration. Euler deconvolution identified shallow to moderately deep magnetic sources concentrated around Itapaji, Bolorunduro, and parts of Ikole. Factor analysis extracted two significant components explaining 92.04% of the total variance, comprising a lithological association (Cu–Ni–Co–Fe–Zn–Mn) and a hydrothermal pathfinder association (As–Th–Ag–Pb). Pearson correlation analysis confirmed strong positive relationships among Cu, Ni, Co, Fe, and Zn, indicating a common geological origin. The integrated interpretation demonstrates that trace element enrichment is spatially associated with major basement structures, confirming structural control of sulphide mineralization. The Itapaji–Bolorunduro corridor and adjoining parts of Ikole were identified as the most prospective exploration targets. The study demonstrates that integrating aeromagnetic and trace element geochemical datasets provides a reliable framework for mineral prospectivity mapping within the Nigerian Basement Complex.