Loud hydroacoustic sources, such as naval mid-frequency sonars or airguns for marine geophysical prospecting, have been increasingly criticized for their possible negative effects on marine mammals and were implicated in several whale stranding events. Competent authorities now regularly request the implementation of mitigation measures, including the shut-down of acoustic sources when marine mammals are sighted within a predefined exclusion zone. Commonly, ship-based marine mammal observers (MMOs) are employed to visually monitor this zone. This approach is personnel-intensive and not applicable during night time, even though most hydroacoustic activities run day and night. This study describes and evaluates an automatic, ship-based, thermographic whale detection system that continuously scans the ship’s environs for whale blows. Its performance is independent of daylight and exhibits an almost uniform, omnidirectional detection probability within a radius of 5 km. It outperforms alerted observers in terms of number of detected blows and ship-whale encounters. Our results demonstrate that thermal imaging can be used for reliable and continuous marine mammal protection.