Northern Chile is a region characterised by an extremely dry climate; however, there is a brief rainy season from December to March (austral summer), mainly above 3000 m a.s.l. It is interesting to consider where the humid air masses that generate such rain come from. For this purpose, daily precipitation data from 161 meteorological stations located in this area (18° S–19° S) were considered, and four clusters formed by k-means clustering. For each cluster, days of extreme precipitation (above 90th percentile) were selected to obtain flow strength (F), direction (D), and vorticity (Z) for each event according to the Jenkinson and Collison (JC) method. The back trajectory, for the previous 72 h, of air masses affecting the centroid of each cluster was determined by means of the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model. The analyses were carried out at sea level (1013 hPa) and in the middle (500 hPa) and upper (250 hPa) troposphere. Surface circulation was not a determining factor in the occurrence of extreme events, but it did influence circulation at 500 and 250 hPa. For stations located in the northern Altiplano, moisture advection from the Amazon basin is evident due to the configuration of the Bolivian high—an upper level anticyclone that develops over the Bolivian Altiplano during austral summer. For stations located in the southern part of the study area, the main source of moisture is the Pacific Ocean, and the weather is related to the arrival of frontal systems and to the configuration of cut-off low pressure systems in the mid-troposphere. The authors want to thank the FONDECYT Project 11160059 of the Chilean Government, the Climatology Group (2017SGR1362, Catalan Government) and the CLICES Project (CGL2017-83866-C3-2-R) for the institutional support. R.S.N. is funded by the Spanish Ministry of Science and Innovation (grant no. FJCI-2017-31595).