This paper examines the response of the upper atmosphere to equatorial Kelvin waves with a period of ~3 days, also known as ultra-fast Kelvin waves (UFKWs). The whole atmosphere model GAIA is used to simulate the UFKW events in the late summer of 2010 and 2011 as well as in the boreal winter of 2012/2013. When the lower layers of the model below 30 km altitude are constrained with meteorological data, GAIA is able to reproduce salient features of the UFKW in the mesosphere and lower thermosphere as observed by the Aura Microwave Limb Sounder. The model also reproduces ionospheric response, as validated through comparisons with total electron content data from the GOCE satellite as well as with earlier observations. Model results suggest that the UFKW produces eastward-propagating ~3-day variations with zonal wavenumber 1 in the equatorial zonal electric field and F-region plasma density. Model results also suggest that for a ground observer, identifying ionospheric signatures of the UFKW is a challenge because of ~3-day variations due to other sources. This issue can be overcome by combining ground-based measurements from different longitudes. As a demonstration, we analyze ground-based magnetometer data from equatorial stations during the 2011 event. It is shown that wavelet spectra of the magnetic data at different longitudes are only in partial agreement, with or without a ~3-day peak, but a spectrum analysis based on multipoint observations reveals the presence of the UFKW.