This study presents an intermingled fractal model capable of simulating the porous microstructure of natural stones used in historical buildings. The developed model is aimed at predicting, by an analytical approach, the sorptivity of these materials. To verify the actual ability of the proposed method to predict stone sorptivity, in this study the intermingled fractal units model was applied to eight types of natural stones. The results are in very good agreement with sorptivity values obtained by experimental tests on the investigated stones. Compared to other analytical formulas proposed in the literature for predicting the sorptivity of porous materials, the newly proposed method better matches with the experimental results, and this can be attributed to that fact it takes into consideration the whole pore size distribution of the analyzed material, rather than the average pore radius only. Thanks to the proposed method, the sorptivity of natural stones used in historical buildings can be calculated from their pore size distribution determined by MIP, which, contrary to standard tests for sorptivity determination, only requires small and irregular samples.