AbstractMidnight and post‐midnight ionospheric irregularities are observed over Brazil sector during the June solstice of solar inactive years. The prevailing nighttime winds in the magnetic meridional plane (magnetic meridional winds) are experimentally described as a trans‐equatorial wind, and superposed a convergent/equatorward component that emerges after 03 LT. Further computation of the growth rate of the generalized Rayleigh‐Taylor (GRT) instability well explains the local time dependent irregularities observed. Our analysis indicates that the trans‐equatorial wind before midnight uplifts the ionosphere in the upwind (northern) hemisphere, whereas the expected downwelling in the conjugate hemisphere is almost unseen. The wind hence decreases the field‐line integrated Pedersen conductivity and promotes the midnight instability, instead of suppressing it as conventionally known. After 03 LT, the convergent/equatorward component also provides an unstable condition, consistent with the theory that a meridional wind profile with a negative latitudinal gradient will destabilize the ionosphere. The growth rate gets lower as the neutral winds weakened with increasing solar activity, but seemingly insufficient to explain the much fewer instabilities observed in 2012 than in 2009. Other solar activity dependent factors need to be taken into account in addition to the growing process of the GRT instability in the F region.