The equatorial region of the Earth’s ionosphere exhibits large temporal variations in electron density that have significant implications on satellite signal transmissions. In this paper, the first observation results of the variations in the trough of the equatorial ionospheric anomaly at the permanent Global Navigation Satellite System (GNSS) site in Chuuk (Geographic: 7.5° N, 151.9° E; Geomagnetic: 0.4° N) are presented. It was found that the daytime Global Positioning System (GPS) total electron content (TEC) values vary according to the 27 day period of solar rotation , and that these trends show sharp contrast with those of summer. The amplitudes of the semi-annual anomaly were 12.4 TECU (33 %) on 19th of March and 8.8 TECU (23 %) on 25th of October respectively, with a yearly averaged value of 38.0 TECU. The equinoctial asymmetry at the March equinox was higher than that at the October equinox rather than the November equinox. Daily mean TEC values were higher in December than in June, which could be interpreted as annual or winter anomalies. The nighttime GPS TEC enhancements during 20:00-24:00 LT also exhibited the semi-annual variation. The pre-midnight TEC enhancement could be explained with the slow loss process of electron density that is largely produced during the daytime of equinox. However, the significant peaks around 22:00-23:00 LT at the spring equinox require other mechanisms other than the slow loss process of the electron density.