This article presents an accurate and robust method to calculate the phase offset of a reference waveform, usually produced by a digital-to-analog converter (DAC) in IEC Std 61850-9-2 calibration systems. The phase offset is defined with respect to the rising edge of a reference clock signal, locked to the Global Positioning System (GPS). The proposed method relies on the synchronous acquisition of the DAC output and the clock signal. In the complex plane, where the discrete Fourier transform (DFT) is defined, the acquired signals are processed to compensate the nonideal sampling rate and windowing. The method performance and its dependence from noise and parameters are thoroughly characterized by means of extensive numerical simulations. Two validation approaches, experimental and software-based, confirm the proposed method as a valuable and robust solution for calibration purposes.