Determination of the sediment fill geometry and structure of basins along the western flank of the Central Andes is crucial for understanding the regional tectonic evolution and the geological situation of natural resources. In this study, we developed a sediment-thickness distribution model for the Pampa del Tamarugal basin (between 20°20′S and 21°30′S, northern Chile), from surface geological information, available wells, and interpretation and depth conversion of 14 seismic-reflection profiles. Four Oligocene–Holocene units and one Carboniferous–Eocene undifferentiated basement unit were identified in the seismic profiles. For depth conversion, we established an empirical velocity model using P-wave velocities measured from rock samples, with velocity values from 2 to 6 km/s. By interpolating the basal-fill surface from the processed data set, and subtracting it from the topographic surface, we generated an isopach map of the basin, which has a maximum fill thickness of 1566 m. Four N-S–elongated asymmetric subbasins with a fill exceeding 700 m in thickness were identified, and these are separated by four basement highs. Both basement and fill units are folded and cut by west-vergent high-angle reverse faults, which originated before the Oligocene and were reactivated in the Miocene. During the isopach map construction, three sources of error were identified (i.e., topographic adjustment, interpretation, and conversion method), and the mean accumulated thickness error was found to be ±250 m; in addition, the lack of wells as validation data also contributes to the uncertainty. Based on our results, the basin-fill geometry was controlled by both compressional tectonics, which generated uplifted blocks and accommodation spaces, and desertification, which has significantly decreased the sediment input since the late Miocene. Despite the uncertainties, our results provide new insights into Andean tectonics and may be used as a screening tool for natural resources such as minerals and groundwater.