In this paper, we present the secrecy performance of a cognitive underlay hybrid radio frequency/free space optical (RF/FSO) system, where the licensed spectrum of a primary user (PU) is shared with the secondary user (SU) and an Eavesdropper attempts to intercept the information through the SU RF sub-link. At the SU receiver, the selection combining scheme with heterodyne detection is considered as signal reception. In order to ensure the required quality of service at the PU, the transmit power constraint of SU RF-sub link is assumed to depend only on the interference level arriving at the PU. It is also assumed that all the system RF links follow the Nakagami-m distribution except the Eavesdropper link that is subjected to Rayleigh fading. The SU FSO link is assumed to undergo Gamma–Gamma distribution with pointing error and link blockage. Thus, the cumulative distribution function (CDF) of the SU RF sub-link is obtained and used to derived the system equivalent CDF. By utilizing system equivalent CDF, the closed-form expressions for the secrecy outage probability and average secrecy capacity are derived through the lower bound. In addition, Monte-Carlo simulation is provided to verify the accuracy of the derived expressions. The results demonstrate the influence of atmospheric turbulence, pointing error, link blockage and average signal to noise ratio at the Eavesdropper on the system performance.