Optical wireless communications in space are degraded by atmospheric turbulence, light attenuation, and detector noise. In this paper, we develop a neural network (NN) channel estimator that is optimized across a wide range of signal-to-noise ratio levels during the training stage. In addition, we propose a novel autoencoder (AE) model to develop a complete physical layer communication system in space optical communications (SOC). The AE is designed to work with both perfect and imperfect channel state information (CSI), providing a flexible and versatile solution for SOC. Batch normalization and multiple-decoders are incorporated into the proposed AE, which improves receiver learning capabilities by allowing the use of more than one path to update encoder and decoder weights. This novel approach can reduce the error in detection relative to state-of-the-art models. Using the system tool kit simulator, we examine our system's performance in a downlink SOC channel that connects a geostationary satellite to a ground station in Log-normal fading channel. Furthermore, we evaluate the performance of our system in a downlink channel that establishes a connection between a Low Earth Orbit satellite and a ground station, operating in Gamma-Gamma fading channel. The numerical results show that the proposed channel estimator NN is superior to state-of-the-art learning-based frameworks and achieves the same level of performance as the minimum mean square error estimator. Additionally, with no fading and for both perfect and imperfect CSI with different code rates and fading channels, the proposed AE-based detection outperforms both benchmark learning frameworks and most popular convolutional codes.INDEX TERMS Deep learning, channel estimation, symbol detection, space optical communications, system tool kit.