An experiment to measure equatorial amplitude scintillations on the geostationary Wide Area Augmentation System (WAAS) Satellite Based Augmentation System (SBAS) signal was conducted in Cachoeira Paulista (22.70°S, 45.01°W geographic coordinates; −17.74°N, 21.74°E geomagnetic coordinates), Brazil from December 2003 through February 2004. The purpose of this paper is to estimate the scattering height of the irregularities using the WAAS signal scintillations as compared to nearby Global Positioning System (GPS) signal scintillations. Estimating the scattering height is important because the calculated zonal drift velocity of the irregularities using the measured scintillation pattern velocity on the ground is height dependent. Accurate height estimation is also required if one wishes to develop phase screen scintillation models. The difference in the pattern velocities is due to the different signal puncture point velocities with respect to the ionospheric drift. Two east-west receivers are used to measure the scintillation pattern drift velocity and to compare the results of the geostationary WAAS satellite signal to that of a GPS satellite signal, which has a nonzero ionospheric signal puncture point velocity. By varying the assumed scattering height for the measurements from the nearby GPS signal, the zonal velocity measurements from the GPS scintillations can be matched to those of the WAAS scintillations, and a scattering height estimate can be made. When the puncture points have minimal separation, the inferred ionospheric irregularity zonal velocities should be equal. On the two nights for which data are available, scattering height estimates of 669 ± 209 km for the first night and 388 ± 139 km for the second night were obtained. On the second night, the reported mean hmF2 as calculated using a collocated Digisonde was 385 ± 17 km over the same period as the GPS/WAAS scattering height estimate. The geometry of this experiment was not optimal, but analysis demonstrates that future experiments could be substantially more accurate.