In this study, we compare the end-to-end performance of optically pre-amplified 16-ary and 64-ary pulse position modulation (PPM) systems for the use in free-space optical communications. Simulations were carried out to evaluate the bit-error-ratio (BER) versus E _b /N ₀ for several scenarios where E _b is the energy per bit and N ₀ is the effective single-sided power spectral density of the noise at the amplifier input. For the optimum full width half maximum (FWHM) of the Fabry-Pérot filter combined with the optimal 3-dB bandwidth of the butterworth electrical filter in the presence of dual polarized amplifier noise and no extinction ratio, the required E _b /N ₀ = 8.37 dB for 16-ary and E _b /N ₀ = 7.1 dB for 64-ary at BER=10 ^-4 . At extinction ratio of 15 dB, the 16-ary PPM system outperforms the 64-ary PPM system with E _b /N ₀ = 10.8 dB for 16-ary and E _b /N ₀ = 12.64 dB for 64-ary since the orthogonality of the M-ary PPM is not maintained any further. The results also indicate that 16-ary PPM systems are more suitable than 64-ary PPM systems for 10 Gbps inter-satellite optical links.