This paper analyzes the physical layer secrecy (PLS) performance of a hybrid free space optical and radio frequency (FSO/RF) communication system under a modified selection combining scheme. The transmission scheme takes into account secrecy performance as well as diversity gain and ease of implementation. The effects of FSO link, namely the FSO atmospheric turbulence and the FSO receiver pointing error, are included in the analysis while the power amplifier (PA) inefficiency for the RF transmission is considered to have more realistic understandings on the system performance. The exact analytical expressions for the performance indicators including the average secrecy capacity (ASC) and secrecy outage probability (SOP) of the investigated mixed FSO/RF system are derived. The asymptotic SOP analysis reveals useful insights into the performance of the investigated mixed system. Analytical and simulation results are presented to evaluate the PLS performance of the proposed mixed system as well as to compare the performance of other hybrid systems with different setups. © 2020 The Author(s)