Abstract The different phases of the Coupled Model Intercomparison Project (CMIP) provide ensembles of past, present, and future climate simulations crucial for climate change impact and adaptation activities. These ensembles are produced using multiple global climate models (GCMs) from different modeling centers with some shared building blocks and interdependencies. Applications typically follow the “model democracy” approach which might have significant implications in the resulting products (e.g., large bias and low spread). Thus, quantifying model similarity within ensembles is crucial for interpreting model agreement and multimodel uncertainty in climate change studies. The classical methods used for assessing GCM similarity can be classified into two groups. The a priori approach relies on expert knowledge about the components of these models, while the a posteriori approach seeks similarity in the GCMs’ output variables and is thus data-driven. In this study, we apply probabilistic network models (PNMs), a well-established machine learning technique, as a new a posteriori method to measure intermodel similarities. The proposed methodology is applied to surface temperature fields of the historical experiments from the CMIP5 multimodel ensemble and different reanalysis gridded datasets. PNMs are able to learn the complex spatial dependency structures present in climate data, including teleconnections operating on multiple spatial scales, characteristic of the underlying GCM. A distance metric building on the resulting PNMs is applied to characterize GCM model dependencies. The results of this approach are in line with those obtained with more traditional methods but have further explanatory potential building on probabilistic model querying. Significance Statement The present study proposes the use of probabilistic network models (PNMs) to quantify model similarity within ensembles of global climate models (GCMs). This is crucial for interpreting model agreement and multimodel uncertainty in climate change studies. When applied to climate data (gridded global surface temperature in this study), PNMs encode the relevant spatial dependencies (local and remote connections). Similarities among the PNMs resulting from different GCMs can be quantified and are shown to capture similar GCM formulations reported in previous studies. Differently to other machine learning methods previously applied to this problem, PNMs are fully explainable (allowing probabilistic querying) and are applicable to high-dimensional gridded raw data.