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Transcranial magnetic stimulation (TMS) is an increasingly popular tool for stroke rehabilitation. Consequently, researchers have started to explore the use of TMS in pediatric stroke. However, the application of TMS in a developing brain with pathologies comes with a unique set of challenges. The effect of TMS-induced electric fields has not been explored in children with stroke lesions. Here, we used finite element method (FEM) modeling to study how the electric field strength is affected by the presence of a lesion. We created individual realistic head models from MRIs (n = 6) of children with unilateral cerebral palsy due to perinatal stroke. We conducted TMS electric field simulations for coil locations over lesioned and non-lesioned hemispheres. We found that the presence of a lesion can strongly affect the electric field distribution. On the group level, the mean electric field strength did not differ between lesioned and non-lesioned hemispheres but exhibited a greater variability in the lesioned hemisphere. Other factors such as coil-to-cortex distance have a strong influence on the TMS electric field even in the presence of lesions. Our study has important implications for the delivery of TMS in children with brain lesions with respect to TMS dosing and coil placement.