Arousals during sleep are transient accelerations of the EEG signal, considered to reflect sleep perturbations associated with poorer sleep quality. They are typically detected by visual inspection, which is time consuming, subjective, and prevents good comparability across scorers, studies and research centres. We developed a fully automatic algorithm which aims at detecting artefact and arousal events in whole-night EEG recordings, based on time-frequency analysis with adapted thresholds derived from individual data. We ran an automated detection of arousals over 35 sleep EEG recordings in healthy young and older individuals and compared it against human visual detection from two research centres with the aim to evaluate the algorithm performance. Comparison across human scorers revealed a high variability in the number of detected arousals, which was always lower than the number detected automatically. Despite indexing more events, automatic detection showed high agreement with human detection as reflected by its correlation with human raters and very good Cohen’s kappa values. Finally, the sex of participants and sleep stage did not influence performance, while age may impact automatic detection, depending on the human rater considered as gold standard. We propose our freely available algorithm as a reliable and time-sparing alternative to visual detection of arousals.