Over the last two decades, free-space optical communication (FSOC) has become more and more interesting as an adjacent and/or alternative to radio frequency (RF) and optical fiber communications. The optical wave propagation in the FSOC channel is severely affected by atmospheric parameters, and it leads to the degradation of the data transmission quality and reliability. Among the various atmospheric effects, the beam wandering is the main cause of major power loss and cannot be solved without the incorporation of the beam centroid stabilization system. Therefore, designing a suitable opto-electronic assembly with a beam wandering mitigation system becomes significant to improve the performance of the FSOC system. A FSOC experimental setup is developed for the link range of 0.5 km in the college campus. A neural controller is designed for beam wandering mitigation. The neural controller processed the beam pointing (beam location) information obtained from an opto-electronic position detector (OPD) and then generated the necessary control outputs to the fast steering mirror (FSM) to steer the beam in the counter-direction to mitigate the beam wander at the receiver station. New design approach and architecture development for the implementation of the designed neural controller in the field-programmable gate array (FPGA) to mitigate the beam wandering are presented. The investigations on the performance of the neural controller in aiming a laser beam to be at a particular point on the detector plane are tested under dynamic disturbances generated at the transmitter in addition to the atmospheric effects through which the maximum correction capability of the developed neural controller is examined. Evidence of the suitability and the effectiveness of the proposed neural controller is evaluated in terms of beam centroid displacement, power spectral density (PSD), radial displacement on a 2D plane, effective scintillation index (ESI), Q-factor, and bit error rate (BER). The beam wandering range of −0.13 to +0.16 mm, maximum of 55 dB disturbance band attenuation with a frequency range of 0 Hz through 2 kHz, ESI of 0 to 0.15, Q-factor of 6, and BER of 6.45 × 10⁻⁹ are achieved due to the incorporation of the developed neural controller in different real-world environmental conditions.