The airborne magnetic data over Afikpo Synclinorium were used to highlight subsurface structures and establish the orientations of tectonic features and their influence on the hydrocarbon play of the area. The characteristic trends of the lineaments were achieved through the center for exploration targeting of grid data analysis. The results of the TMI, residual magnetic field, first vertical, horizontal derivative, Analytic signal, and Tilt angle derivative classified the area into regions of high magnetic intensity observed around the northeastern, southwestern, and central portions of the study area. These areas characterized by anomalous signatures of short magnetic wavelengths delineate shallow magnetic sources. Conversely, regions with medium to low magnetic intensities are characterized by long magnetic wavelengths which indicates deep-seated magnetic source(s) and prospect for hydrocarbon (if other play concepts are emplace); due the thick sediment cover at the southern portion of the area (around, southern part of Nguzu, Ohafia, Biakpan, Abriba and Bende areas). The sediment thickness decreases towards north, west, North-east and north-west (dominated by Benue Trough deposit). Depth to the anomaly sources is of two categories, namely, shallow <1.0 km (dominated by NE trending structures) and deep ≥2.5 km. Ground-truthing confirmed the anomalous zone of high magnetic sources in the northeastern and central regions as Tertiary related tectonic-magmatic intrusion. The most prominent intrusion cuts across Amangwu Edda in Afikpo South through Amaeta-Oziza to Cross River State in a fissure form. This intrusion occurrence conformed to the high magnetic signature identified as a dolerite sill within the Afikpo Sub-basin. It stretches over 16 km in length with an average width of about 1.2 km, having its widest part in the northern parts of Mata Hospital Afikpo. The subsurface topographic model indicated that no fewer than 50% of the study area is characterized by sporadically distributed intrusive rocks. The result revealed several structural lineaments with high lineament density at the northcentral corner of the area trending NE-SW with fault lines (slip fault) perpendicular to it, offsetting the Akpoha, Ibii, Amasiri. and Ozara-ukwu ridges. The major drainage systems across the area followed major structural trends perpendicular to the identified major lineaments, passing through the major regional structural displacement pattern of the Basin. The emplacement of these intrusions might have impacted the hydrocarbon potential of the basin.