The beam motion is one of the main causes for major power loss which severely degrades the performance of the Free Space Optical Communication (FSOC) system. Designing a suitable controller to correct the beam motion to increase the beam stability at a point becomes significant. This paper presents an investigation on the performance of two types of controller designed for aiming a laser beam to be at a particular spot under dynamic disturbances generated at the transmitter. The experimental nonlinear input–output data mapping is used as the principal components for the controller design. The first design is based on the Taguchi method while the second is the artificial neural network—cognitive method. These controllers process the beam pointing (beam location) information from an opto-electronic position detector and then generate the necessary outputs to steer the beam with fast steering mirror. Conceptually, the controller design problem is addressed with looking the position error information to decide the level of nonlinear static output map for generating the correction control information. The pipelined-parallel architecture of both controllers are developed in a field programmable gate array (FPGA) and installed at the receiver station. Evidence of the suitability and the effectiveness of the proposed controller in terms of prediction exactness, response to impulse, scintillation, Q-factor and bit error rate are provided through experimental results obtained from the 155 Mbps FSOC data link set-up established for the horizontal range of 0.5 km at an altitude of 15.25 m.