Southern Tunisia is known to be less deformed and simpler than its neighboring Atlassic domain to the north. This area is complex and basin evolution in the Southern Chotts-Jeffara (SCJ) basin is debated. In this paper we combined surface and subsurface data with low temperature thermochronology (LTT) to reinvestigate the tectono-sedimentary evolution of the SCJ basin from Permian to Jurassic. We reconstruct the present-day architecture of the SCJ basin along two regional sections. In these sections, we focused mainly on regional thickness variations and on internal reflections interpreted from seismic data. We observe three structural elements: (a) A Paleozoic culmination, oriented E-W, capped by Mid-Upper Triassic deposits; (b) the Tebaga of Medenine (ToM), a culmination also oriented E-W but located ∼50 km north of the Paleozoic culmination; and (c) A Triassic culmination in the eastern part of the area, oriented NW-SE. We note the absence of major normal faults along the sections. The LTT data we present are the first published in this area and allow to reconstruct the timing and magnitude of vertical movements. These data prove: (a) exhumation at ∼230 Ma of the Permian and Lower Triassic units associated with the onset of the ToM removing locally about 900 m of pre-Cretaceous sediments; and (b) the development of the Triassic culmination ∼180 Ma removing 2000 m of pre-Cretaceous sediments in the Jebel Rehach. This study demonstrates that vertical movements in the SCJ basin are controlled by long-wavelength processes developed essentially in shortening regimes.