This paper considers the physical layer security (PLS) performance analysis of an unmanned aerial vehicle (UAV)-assisted free-space optical (FSO) communication system over Fisher–Snedecor (F) distributed turbulence fading channel. We consider the combined effects of atmospheric turbulence, pointing error (PE), atmospheric attenuation, and angle-of-arrival (AOA) fluctuations on the channel. The communication between two legitimate peers in the presence of an external eavesdropper is studied from the perspective of communication theory security. Specifically, under two different eavesdropping scenarios where an eavesdropper is located close to the legitimate transmitter or receiver, we derive the exact closed-form expressions of the secrecy outage probability (SOP) and strictly positive secrecy capacity (SPSC), respectively. These analytical results are validated through Monte Carlo simulations. Furthermore, we also analyze the impact of various link parameters for both the main channel and the eavesdropping channel on the system performance.