To investigate the interference effects of lightning on unmanned aerial vehicle (UAV) navigation receivers, an analytical approach for the evaluation of indirect lightning effects is suggested. The blocking mechanism of lightning pulses on the receiver is analyzed using the vector method. A behavioral-level simulation model of the receiver’s radio frequency (RF) front-end is constructed, and a lightning pulse injection simulation is performed based on the advanced design system (ADS). The simulation results indicate that lightning pulses induce blocking interference on the RF front-end of the navigation receiver, reducing its sensitivity and dynamic range. This interference is attributed to gain compression and degradation of the noise figure in the low-noise amplifier (LNA). To further validate the simulation results, a pin injection test is carried out to examine the influence of lightning pulses with different peak voltages on receiver sensitivity. The test results indicate a notable reduction in the receiver sensitivity when the lightning pulse peak reaches 250 V. The sensitivity trends across various test panels are consistent, and the damage thresholds are similar. These findings confirm the accuracy of the simulation results.