We develop an improved application of the mesosphere-stratosphere-troposphere (MST) radar technique for the measurement of winds at ionospheric F region altitudes. While the experiment is basically one of incoherent scatter (IS), which yields very weak signals at the usual operating frequencies of MST radars, we develop an analysis technique that allows the signals to be integrated over the entire F region of the ionosphere to gain sufficient statistical accuracy to compute the “layer wind” accurately. This method is contrasted with the normal IS method of determining winds at discrete heights. The method is applied to data collected with the middle and upper atmosphere radar in Japan, though it is applicable to any MST radar having a comparable or even somewhat smaller power-aperture product and may also be adapted for improved results from mainline IS radars. Using this method, we are able to discuss confidently the geophysical behavior of the wind on individual days, whereas previously we were reluctant to discuss anything but climatological features from data averages.