Monitoring brain activity and associated physiology during the administration of general anesthesia (GA) is pivotal to guarantee postanesthetic health. Clinically, electroencephalogram (EEG) monitoring is a well-established method to guide GA. There are no methods available for monitoring EEG in mice (Mus musculus) during surgery. Non-invasive methods of anesthetic level monitoring are limited to oximetry, capnometry, respiratory rate and the color of the mucous membrane. These methods lack direct access to the brain which is the primary target of GA. 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 with the monitoring system revealed that surgical concentrations of isoflurane anesthesia predominantly contained burst suppression patterns in mice. EEG suppression ratios and durations showed strong correlations with the isoflurane concentrations. The suppression duration in the raw EEG signals during isoflurane anesthesia is an easy-to-detect and reliable marker to assure safe, adequate and reproducible anesthesia protocols.