Non-invasive brain stimulation (NIBS) technologies, such as repetitive transcranial magnetic stimulation (rTMS), offer significant therapeutic potential for a growing number of neuropsychiatric conditions. Concurrent with the expansion of this field is the swift evolution of rTMS methodologies, including approaches to optimize stimulation site planning. Traditional targeting methods, foundational to early successes in the field and still widely employed today, include using scalp-based heuristics or integrating structural MRI co-registration to align the transcranial magnetic stimulation (TMS) coil with anatomical landmarks. Recent evidence, however, supports refining and personalizing stimulation sites based on the target's structural and/or functional connectivity profile. These connectomic approaches harness the network-wide neuromodulatory effects of rTMS to reach deeper brain structures while also enabling a greater degree of personalization by accounting for heterogenous network topology. In this study, we acquired baseline multimodal magnetic resonance (MRI) at two time points to evaluate the reliability and reproducibility of distinct connectome-based strategies for stimulation site planning. Specifically, we compared the intra-individual difference between the optimal stimulation sites generated at each time point for (1) functional connectivity (FC) guided targets derived from resting-state functional MRI and (2) structural connectivity (SC) guided targets derived from diffusion tensor imaging. Our findings suggest superior reproducibility of SC-guided targets. We emphasize the necessity for further research to validate these findings across diverse patient populations, thereby advancing the personalization of rTMS treatments.