Mountain permafrost and rock glaciers in the dry Andes are of growing interest due to the increase in mining industry and infrastructure development in this remote area. Empirical models of mountain permafrost distribution based on rock glacier activity status and temperature data have been established as a tool for regional-scale assessments of its distribution; this kind of model approach has never been applied for a large portion of the Andes. In the present study, this methodology is applied to map permafrost favourability throughout the semi-arid Andes of central Chile (29–32°S), excluding areas of exposed bedrock. After spatially modelling of the mean annual air temperature distribution from scarce temperature records (116 station years) using a linear mixed-effects model, a generalized additive model was built to model the activity status of 3524 rock glaciers. A permafrost favourability index (PFI) was obtained by adjusting model predictions for conceptual differences between permafrost and rock glacier distribution. The results indicate that the model has an acceptable performance (median AUROC: 0.76). Conditions highly favourable to permafrost presence (PFI  ≥ 0.75) are predicted for 1051km2 of mountain terrain, or 2.7% of the total area of the watersheds studied. Favourable conditions are expected to occur in 2636km2, or 6.8% of the area. Substantial portions of the Elqui and Huasco watersheds are considered to be favourable for permafrost presence (11.8% each), while in the Limarí and Choapa watersheds permafrost is expected to be mostly limited to specific sub-watersheds. In the future, local ground-truth observations will be required to confirm permafrost presence in favourable areas and to monitor permafrost evolution under the influence of climate change.