Objective: Large structural brain changes, such as chronic stroke lesions, alter the current pathways throughout the patients’ head and therefore have to be taken into account when performing transcranial direct current stimulation simulations. Approach: We implement, test and distribute the first MATLAB pipeline that automatically generates realistic and individualized volume conduction head models of chronic stroke patients, by combining the already existing software SimNIBS, for the mesh generation, and LINDA, for the lesion identification. To highlight the impact of our pipeline, we investigated the sensitivity of the electric field distribution to the lesion location and lesion conductivity in 16 stroke patients’ datasets. Main results: Our pipeline automatically generates 1 mm-resolution tetrahedral meshes including the lesion compartment in less than three hours. Moreover, for large lesions, we found a high sensitivity of the electric field distribution to the lesion conductivity value and location. Significance: This work facilitates optimizing electrode configurations with the goal to obtain more focal brain stimulations of the target volumes in rehabilitation for chronic stroke patients.