In this research paper, the sub-surface heat flow of a part of the Chad Basin, in North eastern Nigerian was estimated using spectral analysis. This was obtained from twenty (20) digitized High Resolution Aeromagnetic (HRAM) data sheet covering the study area. Regional-residual separation using first order polynomial fitting method with three coefficients was carried out on the data map before the application of statistical spectral analysis. Result shows that the centroid depth varies between 9.39 km and 18.31 km. The depth to the Curie temperature isotherm varies between 15.14 km and 33.46 km below the mean sea level. It was also found that the Curie temperature isotherm within the basin is not a horizontal level surface but an undulating surface with geothermal gradients and heat flow ranging between 15.77 and 38.31˚C/Km, and 39.41 and 95.77 respectively. Thus, the calculated average geothermal gradient and heat flow for this area are 23.39˚C/Km and 58.47 respectively. Since average heat flow in thermally normal continental region is 60 and the values in excess of 80-100 are associated with anomalous geothermal conditions, hence the study area can generally be considered as a thermally normal region. But, the northeastern part of the study area with values in excess of 80 is recommended for further investigation.