The potential clinical applications of adaptive neural network control for pharmacology in general, and anesthesia and critical care unit medicine in particular, are clearly apparent. Specifically, monitoring and controlling the levels of consciousness in surgery is of particular importance. Nonnegative and compartmental models provide a broad framework for biological and physiological systems, including clinical pharmacology, and are well suited for developing models for closed-loop control of drug administration. In this paper, we develop a neural adaptive output feedback control framework for adaptive set-point regulation of nonlinear uncertain nonnegative and compartmental systems. The proposed framework is Lyapunov-based and guarantees ultimate boundedness of the error signals corresponding to the physical system states and the neural network weighting gains. The approach is applicable to nonlinear systems with unmodeled dynamics of unknown dimension and guarantees that the physical system states remain in the nonnegative orthant of the state space for nonnegative initial conditions.