We present a non-equilibrium analysis and control approach for the Active Queue Management (AQM) problem in communication networks. Using simplified fluid models we carry out a bifurcation study of the complex dynamic queue behavior to show that non-equilibrium methods are essential for analysis and optimization in the AQM problem. We investigate an ergodic theoretic framework for stochastic modeling of the non-equilibrium behavior in deterministic models and use it to identify parameters of a fluid model from packet level simulations. For computational tractability, we use set-oriented numerical methods to construct finite-dimensional Markov models. Subsequently, we develop and analyze an example AQM algorithm using a Markov Decision Process (MDP) based control framework. The control scheme developed is optimal with respect to a reward function defined over the queue size and aggregate flow rate. We implement and simulate our illustrative AQM algorithm in the ns-2 network simulator. The initial results obtained confirm the theoretical analysis and exhibit promising performance when compared with well-known alternative schemes under persistent non-equilibrium queue behavior.