The zebrafish model has been demonstrated as an ideal vertebrate model system for a diverse range of biological studies. Along with conventional approaches, monitoring and analysis of zebrafish electrocardiogram (ECG) have been utilized for cardio-physiological screening and elucidation. ECG monitoring has been carried out with fish treated with anesthetic drugs, rendering the short period of time in recording the signals (<5 min). In this work, a prolonged sedation system for continuous ECG monitoring of multiple zebrafish was proposed and developed. We built a circulation system to provide prolonged mild anesthesia which allows more consistent and intrinsic ECG measurement. The use of prolonged anesthesia helped reduce the concentration of the anesthetic drug (MS222 or Tricaine) from 200 mg/L to 100 mg/L and even lower; thus, maintaining the integrity of intrinsic ECG. Moreover, heartrate variation during recording was investigated, showing minute changes (±3.2 beats per minute - BPM). The development of this prolonged ECG monitoring system would open the possibility of long-term monitoring for studies such as drug screening and forward genetic screening.