Monitoring brain activity and associated physiology during the administration of general anesthesia (GA) in mice is pivotal to guarantee postanesthetic health. Clinically, electroencephalogram (EEG) monitoring is a well-established method to guide GA. There are no established methods available for monitoring EEG in mice (Mus musculus) during surgery. In this study, a minimally invasive rodent intraoperative EEG monitoring system was implemented using subdermal needle electrodes and a modified EEG-based commercial patient monitor. EEG recordings were acquired at three different isoflurane concentrations revealing that surgical concentrations of isoflurane anesthesia predominantly contained burst suppression patterns in mice. EEG suppression ratios and suppression durations showed strong positive correlations with the isoflurane concentrations. The electroencephalographic indices provided by the monitor did not support online monitoring of the anesthetic status. The online available suppression duration in the raw EEG signals during isoflurane anesthesia is a straight forward and reliable marker to assure safe, adequate and reproducible anesthesia protocols.