The Faghur-Siwa Basin is a large sedimentary basin in the westernmost region of the Egyptian Western Desert. The northern portion of this basin has been hydrocarbon productive for the last few decades, making it a subject of frequent geological and geophysical studies. The current study aims to outline the subsurface extent, geometry and structural framework of Southern Faghur-Siwa Basin. The study introduces an approach of using large data set to deduce the structural setting of a sedimentary basin and its applicability to large-scale tectonic features in similar regions worldwide. This study uses satellite-derived potential field data, data of deep wells penetrating the basement, and previous geological studies. The Gaussian filter with a cut-off wave number of 0.0225 (Radian/km) was applied to study deep and shallow anomaly sources in the area while the edge detection methods were used to outline the subsurface boundaries of these sources. The 2.5D forward modeling of magnetic and gravity delineated the basin geometry and basement depth that ranges from 1200 to 5100 m. The basement structure map created by this study showed a complex subsurface structural framework of the Southern Faghur-Siwa Basin that is dominated by N–S, NNW-SSW, NE-SW, and E-W trending faults. •Southern Faghur-Siwa Basin has an N–S axis, 500 km length, and 100–300 km width.•Mafic intrusions underlie the northern, eastern, and western parts of the basin.•Felsic igneous rocks underlie the central and southern parts.•2.5D gravity and magnetic models reveal basement depths ranging from 1200 to 5100m.•The basin is connected to Kufra Basin from the west and Abu Tarture Basin from east.