We analyze the propagation of equatorial Kelvin waves from the troposphere to the stratosphere using a new filtering technique applied to ERA-Interim data (very similar results for Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) temperatures) that allows separation of wave activity into number of waves and wave amplitude. The phase speed of Kelvin waves (order 20 m/s) is similar to the magnitude of zonal wind in the tropical tropopause layer (TTL), and correspondingly, we find that the seasonal and interannual variability of Kelvin wave propagation is dominated by the variability in the wind field and less by tropospheric convectively coupled wave activity. We show that local relations between wave activity and zonal wind are ambiguous, and only full ray tracing calculations can explain the observed patterns of wave activity. Easterlies amplify and deflect the eastward traveling waves upward. Westerlies have the opposite effect. During boreal winter, the strong dipole of zonal winds in the TTL centered at the dateline confines wave propagation into the stratosphere to a window over the Atlantic-Indian Ocean sector (30°W to 90°E), which casts a lasting “shadow” into the lower stratosphere that explains the remarkable zonal asymmetry in wave activity there. During boreal summer, the upper level monsoon circulation leads to maximum easterlies, and wave amplitude (but not number of waves) maximizes over the Indian Ocean sector (30°E to 90°E). Interannual variability in wave propagation due to El-Niño/Southern Oscillation, for example, is well explained by its modification of the zonal wind field.