The synchronization of radio frequency (RF) systems in hadron synchrotrons relies on the availability of reference RF signals with a precise phase. For accelerators with a large frequency swing, frequency dependent phase errors can exceed the required phase margin and therefore have to be compensated. In this paper a new method for the phase calibration of RF signals with variable frequency is described. All the signals are measured with a digital oscilloscope and no complex signal processing is necessary. The described approach utilizes a three-parameter sine wave fit algorithm to estimate the phase of the relevant sine wave signals. A phase difference between RF signals with different frequencies is then calculated with respect to a reference pulse train. A detailed analysis of the measurement parameters is given. The method is applied for the calibration of the RF reference signals of the heavy ion synchrotron SIS18 at GSI.