The GPS radio occultation (RO) of FORMOSAT-3/COSMIC (F3/C) with 1–2.5-km-altitude resolution is used to scan fluctuations on vertical profiles of the ionospheric electron density induced by seismic and tsunami waves of the March 11, 2011 M9.0 Tohoku earthquake. The Hilbert–Huang transform is applied to derive the instantaneous wave number and amplitude of the fluctuations in 22 (7 before and 15 after) F3/C profiles within 3000 km in radius from the epicenter during the earthquake. Fluctuations of the vertical electron density profile induced by underneath Rayleigh and tsunami waves and their post-waves are examined. It is found that the right underneath Rayleigh wave can induce significant long-wavelength fluctuations of 50–105 km on the vertical profile of the electron density, while tsunami and their post-waves activate the prominent short-wavelength fluctuations less than 16 km on those profiles in the poleward side of the epicenter. Results show that RO is a powerful tool which is suitable to probe vertical fluctuations in the ionospheric electron density.