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The aeromagnetic data (High resolution) over part of Bornu Basin NE was interpreted using spectral analysis to estimate the sedimentary thickness of the study area. The study area is covered by four aeromagnetic data sheets covering latitude 12°N and 13°N and Longitude 12°E and 13°E with an estimated total area of 12, 100 km2. Polynomial fitting method was adopted for the regional-residual separation of the total magnetic intensity. The residual map was divided into nine spectral sections. The result of the study shows a sedimentary thickness that ranges between 0.29 km and 3.35 km. The sedimentary thickness of over 3 km could be found around the South-eastern part of the study area which corresponds to Gubio town while the minimum sedimentary thickness could be found around North-western part of the study area which also corresponds to Borgo town area. The maximum sedimentary thickness of 3.35 km may be sufficient for hydrocarbon presence.