This study uses multi‐station time‐domain very‐low and low‐frequency (VLF/LF) lightning waveforms detected from a range of several hundred kilometers to probe fluctuations in D‐layer ionospheric height and peak reflection ratio in three regions near a large thunderstorm on the night of 17 June 2005. These measurements show propagation of the fluctuations away from the thunderstorm in addition to a background eastward‐propagating fluctuation over the entire region. Measured speeds of propagation range from ∼45 m/s to ∼85 m/s, consistent with horizontal propagation speeds of atmospheric gravity waves. The fluctuation propagation is seen in both the ionospheric height measurement and the peak reflection ratio measurement with similar periods and speeds. Ionospheric height perturbations in the measured regions can be as large as 6 km from average, and perturbations in peak reflection ratio can be as large at 100%. Key Points D‐layer disturbances are detected propagating outward from thunderstorm region A new VLF probing technique is used with high temporal and spatial‐resolution Background atmospheric gravity waves cause large scale disturbances in D‐layer