Field-aligned density irregularities (FAI) with kilometer-scale sizes transverse to the background magnetic field are a common feature in the ionosphere at all latitudes and local times. In this paper, we investigate the effect of these irregularities on the transionospheric propagation of very low frequency whistler waves and develop a quantitative description of FAI-related effects on whistler propagation through the lower ionosphere. Using an electron magnetohydrodynamics simulation, we provide two applications of our model. First, we show that the presence of kilometer-scale FAI in the ionosphere can reduce the power observed in the equatorial magnetosphere by more than 10 dB in some cases. Second, we demonstrate that multiple FAIs can act as a discrete lens for whistlers, providing a possible means for increasing wave power in artificial whistler ducting experiments.