For free-space optical communication links where platform size, weight, and power (SWaP) tend to be at a premium, it is important to design transmitters and receivers that can operate as close as possible to the theoretical best performance. For variable duty-cycle, multi-rate optical communication systems, as demonstrated in the NASA LCRD program, finite extinction ratio can become a significant contributor to transmitter implementation loss when the duty cycle becomes low. The ability to measure waveform extinction ratio of a transmitter with high-fidelity is important for the optimization of these transmitter designs. We present a new technique to measure the extinction ratio of a variable duty-cycle transmitter using an intradyne coherent receiver to capture the full electric field of the transmitter. Average power within a burst of data and within the dead-time of the waveform are separately calculated by gating in the time domain and then by filtering in the frequency domain. Our results show that extinction ratios as high as 45 dB can be accurately measured using this technique. We discuss how to choose the optimal bandwidth for integrating power in the frequency domain. Finally, we show the effects of signal-to-noise ratio on the fidelity of the extinction ratio measurement.