Key Points: • Gravity waves impacts in the anomalous responses of the F layer over Brazil during a counter electrojet event; • Some signatures in ionograms suggest the gravity wave as responsible for the CEJ occurrence in this day. Abstract In this work, we report the ionospheric F-layer responses over the Brazilian equatorial sector to a counter electrojet (CEJ) event that occurred during the solar minimum period of June 2009. The data collected by the Digisonde over São Luis (2.33° S; 44° W; dip in 2009:-5.7°) showed a strong modification in the ionospheric F 2 layer trace, that in this case appeared to be “broken in half”. In this process, the first part of the F 2 layer (lower frequency) was thrown down whilst the upper part remained at higher altitudes. Such characteristics occurred simultaneously with an abrupt decrease in the strength of equatorial electrojet and with intensification in the auroral activity. The origin of this phenomenon seems to have a local nature and seems not to be connected to any magnetic disturbance since similar responses were not observed in other longitudinal and latitudinal sectors. Excluding this possibility, we assume that the strong changes observed in the F layer over São Luis had been caused probably by the gravity wave (GWs) propagation, as seen in the downward phase propagation of the altitude contours with time over São Luis and Fortaleza and the remarkable signatures in ionograms over both regions, such as the forking traces that are typically caused by GWs.