Abstract. The All-Sky interferometric meteor (SKYiMET) radar (MR) derived winds in the vicinity of the equatorial electrojet (EEJ) are discussed. As Thumba (8.5° N, 77° E; dip lat. 0.5° N) is under the EEJ belt, there has been some debate on the reliability of the meteor radar derived winds near the EEJ height region. In this regard, the composite diurnal variations of zonal wind profiles in the mesosphere-lower thermosphere (MLT) region derived from TIMED Doppler Interferometer (TIDI) and ground based meteor radar at Thumba are compared. In this study, emphasis is given to verify the meteor radar observations at 98 km height region, especially during the EEJ peaking time (11:00 to 14:00 LT). The composite diurnal cycles of zonal winds over Thumba are constructed during four seasons of the year 2006 using TIDI and meteor radar observations, which showed good agreement especially during the peak EEJ hours, thus assuring the reliability of meteor radar measurements of neutral winds close to the EEJ height region. It is evident from the present study that on seasonal scales, the radar measurements are not biased by the EEJ. The day-time variations of HF radar measured E-region drifts at the EEJ region are also compared with MR measurements to show there are large differences between ionospheric drifts and MR measurements. The significance of the present study lies in validating the meteor radar technique over Thumba located at magnetic equator by comparing with other than the radio technique for the first time.