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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., Accepted in JGR Space Physics