Transcranial magnetic stimulation (TMS) is a non-invasive method that can be used as an interventional technique to investigate causality in the brain-behavior relationship, through depolarization or hyperpolarization in the neurons of the brain. Different techniques of TMS can be used to investigate causality in the brain-behavior relationship. The behavioral effects induced by TMS are complex since it has been shown that the performance in the same cognitive task can be either facilitated or inhibited depending on the area being stimulated. To date, most studies involving TMS are focused mainly on the facilitation properties of this technique. It is used to treat a wide-range of neurological and psychiatric conditions such as depression, ischemia, Alzheimer's disease, or motor impairment. Interestingly, TMS can be used to induce a virtual lesion that could provide a valuable and much needed model of cognitive impairments in early preclinical development. This review describes the existing TMS paradigms in rodents and the major challenges that were encountered by the researchers as the method was translated from clinical to preclinical applications. In summary, the existing knowledge gained in animal research emphasizes the necessity to investigate new TMS paradigms in the preclinical setting and its effects.