Repetitive Transcranial Magnetic Stimulation (rTMS), a non-invasive brain modulation technique, has been explored as an additional treatment option for behaviorally disordered dogs. For optimal effectiveness of the rTMS treatment, accurate coil positioning to the stimulation target is pivotal. Frameless stereotactic neuronavigation for the localization of intracranial regions has been established as a reliable targeting method. However, given the varying skull shape and brain structures among dog breeds, divided into mesocephalic, brachycephalic, and dolichocephalic breeds, localizing the rTMS target area, the central left frontal cortex, can be challenging. Previous neuronavigation studies have only investigated its use in mesocephalic breeds of dogs. Because this neuronavigation is based on expensive high-tesla magnetic resonance imaging data, and anesthesia needed for immobilization, a cheaper and reliable localization alternative to broaden the rTMS use in the veterinary field is needed.The objective of this study was twofold. First, the study aimed to evaluate external localization of the central left frontal cortex within the three skull types (retrospective study 1). Then, this external localization method was compared to the conventional frameless neuronavigation technique to check the consistency, focusing on mesocephalic and dolichocephalic breeds (prospective study 2). Thirty-two brachycephalic, thirty-seven mesocephalic and thirty dolichocephalic dogs were included to evaluate the external localization of the central left frontal cortex by external measurement (retrospective study 1, data obtained from previously performed MRI scans). For the second objective, thirty-eight dogs (35 mesocephalic breeds and 3 dolichocephalic breeds) were recruited to compare the external measurement localization method and the localization by neuronavigation (prospective study 2, data extracted from study 1 and former rTMS studies). The first part of this study showed the central left frontal cortex was externally located approximately two-thirds of the total skull length (sagittal length) in meso- and dolichocephalic dogs, at the center of the skull length in brachycephalic dogs, and 0.65 to 0.70 cm to the left of the cerebral midline for all skull types (retrospective study 1). Using intraclass correlation coefficient (ICC) analysis, the second part of the study showed high consistency between these two methods, for the length of the skull (0.94), the relative position of the left frontal cortex (0.84), and the distance to the cerebral midline (0.69) in mesocephalic and dolichocephalic breeds (prospective study 2). Our findings suggest that the conventional frameless neuronavigation could be replaced by the external localization method in the mesocephalic and dolichocephalic dog breeds, and therefore ultimately reduce anesthesia time and financial burden when applying non-invasive brain modulation techniques like rTMS. More research needs to be conducted for brachycephalic dogs to validate this method in this specific population of dogs.