The purpose of this study was to develop a new approach for the identification of the epileptogenic focus using Blood Oxygen Level Dependent (BOLD) signals from functional magnetic resonance imaging (fMRI) data. This novel approach is based on the following hypotheses (1) the epileptogenic focus BOLD signal during the interictal state shows transient peaks of activation, which differentiate it from signals of the remaining brain; (2) the epileptogenic focus BOLD signal is less complex than those of the remaining brain. A bi-dimensional temporal clustering analysis, a data-driven technique, was used to identify brain regions with similar temporal profiles. Then, the BOLD signals of these regions were assessed regarding complexity using detrended fluctuation analysis and also using a modified multiscale entropy algorithm in order to identify which of those regions corresponded to epileptogenic tissue. In order to demonstrate the applicability of the developed method three epileptic patients were analyzed comprising two types of epilepsy: unilateral and bilateral temporal lobe epilepsies. The results showed that this method is able to detect the brain regions associated with epileptogenic tissue. The results also showed that the epileptogenic focus influences the dynamics of related brain networks. This could be a key factor in the applicability of this method to other epilepsy cases.