Here we test the precursory enhancement in ionospheric total electron content (TEC) which has been reported by Heki (2011) and numerous Global Navigation Satellite System (GNSS) TEC observational studies before the 2011 Mw9.0 Tohoku-Oki and many great earthquakes. We verify the frequency of this TEC enhancement via analysis of a two-month vertical TEC (VTEC) time series that includes the Tohoku-Oki Earthquake using the procedure, based on Akaike’s information criterion, and threshold of Heki and Enomoto (2015). The averaged occurrence rate of the TEC enhancement is much larger than that reported by Heki and Enomoto (2015) when all of the visible GPS satellites at a given station are taken into account. We cannot rule out the possibility that the pre-seismic VTEC changes before the great earthquakes that were reported by Heki and Enomoto (2015) are not precursors but just a product of chance. We also analyze the spatial distribution of the pre-seismic TEC enhancement and co-seismic TEC depletion for the Tohoku-Oki Earthquake with the data after reducing inter-trace biases. We observe significant post-seismic depletion that lasted at least 2 h after the earthquake and extended at least 500 km around the center of the large-slip area. This means that evaluation of the enhancements using reference curves which was adopted by Heki 2011 and even by the recent papers (e.g. He and Heki 2016, 2017, 2018) is in danger of mistaking a large and long-lasting post-seismic TEC depletion for a pre-seismic enhancement.