AbstractFractured porous media challenge modeling approaches due to high computational costs and excessive mesh refinement imposed by the extreme scale variability of fractures and the heterogeneity of the surrounding porous rock. To overcome such difficulties, we utilize the hierarchical finite element method (Hi‐FEM) that has been developed previously to simulate the electrical potential distribution in complex geologic environments. The method employs the hierarchical basis functions in classical finite element analysis to enable representation of material properties on each dimensional component of a given 3D unstructured finite element, thereby inherently allowing for interactions at the boundary between fracture and a host rock. In this study, we extend its application to transient fluid flow and heat conduction in the Laplace domain. Time‐domain flow solutions are obtained by numerical inverse Laplace transform. We evaluate the accuracy of the method using different flow models and demonstrate its robustness for large‐scale, rock mass models featuring complex fracture networks. Moreover, for the computation of nodal Darcian velocity fields in fractured porous media where the fractures are represented as 2D features, a new approach that employs the Yeh's Galerkin model for both volume and facet elements is proposed. Results show that Hi‐FEM can produce accurate flow solutions for fractured porous media without any need of coupling or transfer mechanism while still being computationally economical and numerically robust, even for large‐scale simulations.