An apparatus and method for disinfecting a cryostat is provided. The cryostat disinfecting device comprises an ultraviolet emitter, a pulsed power control system, a mirrored cover and a safety shield. The device is lowered into a cryostat chamber and produces high intensity pulsed UV energy, disinfecting the cryostat chamber. After disinfection, the device is removed from the cryostat for storage or use on another cryostat. This provides mobility and access for disinfecting cryostats under continuous daily use conditions, and reduces the exposure risk of biological and chemical hazards to the operator.