Free space optical communication system (FSO) is a potential solution for increasing bandwidth demands. The FSO has a capability to provide high speed data communication, economic and quick deployable. Although FSO has several advantages, but at the same time FSO faces a major challenge from scintillation introduced by atmospheric turbulence. In this paper, the simulation performance for the binary pulse position modulation (BPPM) system is done under weak and strong atmospheric turbulence. The performances are analyze in terms of bit error rate (BER) and eye diagrams. The system use avalanched photodiode (APD) receiver. The simulation was verified with ideal calculated performance for BPPM. The results show the simulation system is capable to give the BER similar like mathematical model and give the optimum gain of APD to achieve the best BER in atmospheric turbulence environment. The optimum gain for APD result from the simulation for weak turbulence is 150-165 and 160 for strong turbulence. Index Terms-Atmospheric Turbulence, Avalanche Photodiode, Binary Pulse Position Modulation, Free Space Optical Communication Systems.