The formation of continental rift systems is characterised by the interplay of magmatic and tectonic processes. Their evolution involves a wide range of time scales, from centennial scales of the seismic and diking cycles to strain localisation during millions of years of continental thinning. Our understanding of rift processes at different spatial and time scales is limited by relatively short temporal coverages of geophysical measurements and by spatially discontinuous geological datasets. Here we propose a novel method for the automatic extraction of faults and the calculation of time-averaged strains distributions using topographic information from Digital Elevation Models. We apply this method to map ~4000 individual faults within a ~70 thousand km<sup>2</sup> area of the Afar rift (East Africa), where the Nubian, Arabian and Somalian plates diverge. By comparing our results to rock dating and recent decadal geodetic measurements we deduce the rift's deformation history since 4.5 Ma and study its relationship with the current tectonic and magmatic activity. We show that the external portions of the Central Afar rift are not the mail locus of strain and rifting processes have migrated toward the axis where magma emplacement focusses strain rates due to the mechanical and thermal weakening of the crust. Increasing strains toward north-west suggest a progressive migration of the rifting process in the same direction. Conversely, Southern Afar is characterized by two systems of cross-cutting faults that respond to different strain regimes driven by the separations of the Arabian and Somalian plates from Nubia. This study demonstrates the effectiveness of our new method in quantifying fault activity and strain distribution in extensional settings and provides new insights into the spatial and temporal evolution of rifting in Afar.