Epilepsy represents the most prevalent neurological disease in the world. One-third of people suffering from mesial temporal lobe epilepsy (MTLE) exhibit drug resistance, urging the need to develop new treatments. A key part in anti-seizure medication (ASM) development is the capability of detecting and quantifying epileptic seizures occurring in electroencephalogram (EEG) signals, which is crucial for treatment efficacy evaluation. In this study, we introduced a seizure detection pipeline based on deep learning models applied to raw EEG signals. This pipeline integrates: a new pre-processing technique which segments continuous raw EEG signals without prior distinction between seizure and seizure-free activities; a post-processing algorithm developed to reassemble EEG segments and allow the identification of seizures start/end; and finally, a new evaluation procedure based on a strict seizure events comparison between predicted and real labels. Models training have been performed using a data splitting strategy which addresses the potential for data leakage. We demonstrated the fundamental differences between a seizure classification and a seizure detection task and showed the differences in performance between the two tasks. Finally, we demonstrated the generalization capabilities across species of our best architecture, combining a Convolutional Neural Network and a Transformer encoder. The model was trained on animals’ EEGs and tested on humans’ EEGs with a F1-score of 93% on a balanced Bonn dataset.