The performance of the robotic manipulator is negatively impacted by outside disturbances and uncertain parameters. The system’s variables are also highly coupled, complex, and nonlinear, indicating that it is a multi-input, multi-output system. Therefore, it is necessary to develop a controller that can control the variables in the system in order to handle these complications. This work proposes six control structures based on neural networks (NNs) with proportional integral derivative (PID) and fractional-order PID (FOPID) controllers to operate a 2-link rigid robot manipulator (2-LRRM) for trajectory tracking. These are named as set-point-weighted PID (W-PID), set-point weighted FOPID (W-FOPID), recurrent neural network (RNN)-like PID (RNNPID), RNN-like FOPID (RNN-FOPID), NN+PID, and NN+FOPID controllers. The zebra optimization algorithm (ZOA) was used to adjust the parameters of the proposed controllers while reducing the integral-time-square error (ITSE). A new objective function was proposed for tuning to generate controllers with minimal chattering in the control signal. After implementing the proposed controller designs, a comparative robustness study was conducted among these controllers by altering the initial conditions, disturbances, and model uncertainties. The simulation results demonstrate that the NN+FOPID controller has the best trajectory tracking performance with the minimum ITSE and best robustness against changes in the initial states, external disturbances, and parameter uncertainties compared to the other controllers.