The Eye Fixation Related Potential (EFRP) estimation is the average of EEG signals across epochs at ocular fixation onset. Its main limitation is the overlapping issue. Inter Fixation Intervals (IFI) - typically around 300 ms in the case of unrestricted eye movement- depend on participants’ oculomotor patterns, and can be shorter than the latency of the components of the evoked potential. If the duration of an epoch is longer than the IFI value, more than one fixation can occur, and some overlapping between adjacent neural responses ensues. The classical average does not take into account either the presence of several fixations during an epoch or overlapping. The Adjacent Response algorithm (ADJAR), which is popular for event-related potential estimation, was compared to the General Linear Model (GLM) on a real dataset from a conjoint EEG and eye-tracking experiment to address the overlapping issue. The results showed that the ADJAR algorithm was based on assumptions that were too restrictive for EFRP estimation. The General Linear Model appeared to be more robust and efficient. Different configurations of this model were compared to estimate the potential elicited at image onset, as well as EFRP at the beginning of exploration. These configurations took into account the overlap between the event-related potential at stimulus presentation and the following EFRP, and the distinction between the potential elicited by the first fixation onset and subsequent ones. The choice of the General Linear Model configuration was a tradeoff between assumptions about expected behavior and the quality of the EFRP estimation: the number of different potentials estimated by a given model must be controlled to avoid erroneous estimations with large variances.