Solar flare emission at X-ray and extreme ultraviolet (EUV) energies can cause substantial enhancements in the electron density in the Earth's lower ionosphere. It is now become clear that flares exhibit quasi-periodic pulsations with timescales of minutes at X-ray energies, but to date, it has not been known if the ionosphere is sensitive to this variability. Here, using a combination of Very Low Frequency (24 kHz) measurement together with space-based X-ray and EUV observations, we report pulsations of the ionospheric D-region, which are synchronized with a set of pulsating flare loops. Modeling of the ionosphere show that the D-region electron density varies by up to an order of magnitude over the timescale of the pulsations (\(\sim\)20 mins). Our results reveal that the Earth's ionosphere is more sensitive to small-scale changes in solar soft X-ray flux than previously thought, and implies that planetary ionospheres are closely coupled to small-scale changes in solar/stellar activity.