The novelty of this work is the development of a new fractional boundary element model based on the Caputo derivative to investigate anomalous thermal stress effects on cement-based materials. To obtain the BEM integral equations for the proposed formulation, we employ the weighted residuals technique, with the anisotropic fundamental solution serving as the weighting function in the anomalous heat governing equation. The Caputo fractional derivative was employed as an integrand for the domain integral of the proposed formulation. The time step selection is less dependent on the time derivative order. This allows the approach to overcome the non-locality of the fractional operators. The key benefit provided by the suggested formulation is the ability to analyze situations with tiny values of the fractional time derivative. The current BEM methodology proves that it is a useful tool for solving fractional calculus problems.