In this paper, Polar codes are used to mitigate the fading effect caused by atmospheric turbulence (scintillation) in free space optical (FSO) communication channels. We evaluate the bit-error-rate (BER) performances of FSO system with Polar codes under log-normal distributed channel model. Bhattacharyya and Polar weight parameters are used to adapt the FSO channel variations. We perform a series of simulations for several FSO channel parameters. The results show that the performances of Polar codes with Bhattacharyya and Polar weight parameters are similar, because FSO channel has characteristic like AWGN channel, where the channel variation is still weak compared to the variation in Rayleigh fading channels. Given the results, the Polar codes with Bhattacharyya parameters can be applied without further modifications for systems under FSO channels, however, Polar codes with Polar weight are still preferable under Rayleigh fading channels.