A sample preparation apparatus, comprising: an ultrasonic vibrating unit which applies ultrasonic vibration to a sample including an analyte held in a measurement sample container; a sample preparation unit which prepares a measurement sample by mixing the sample including the analyte to which the ultrasonic vibration is applied and a predetermined reagent; and a container transporting unit which transports the measurement sample container holding the sample including the analyte from the ultrasonic vibrating unit to the sample preparation unit.