Since the collapse of the Tacoma Narrows Bridge more than 70 years ago suppressing wind-induced instabilities has been a key aspect of the design of long-span bridges. The intensive experimental and theoretical research in wind engineering allowed researchers and practitioners to not only understand the physics of aeroelastic instability phenomena such as flutter, but also to develop reliable testing procedures, models, and design rules for preventing these instabilities during the lifetime of a bridge. As a consequence, the civil engineering community has adopted a series of design standards for wind effect mitigation of long-span bridges typically called passive measures. A passive solution, although safe in respect to wind perturbations, is intrinsically a static compromise for a dynamic system response to a variable and uncertain perturbation and as such it implies numerous limitations. Therefore, in the last two decades researchers have investigated active measures for preventing aeroelastic instabilities, especially flutter. The underlying motivation is that an active damping mechanism can adapt to dynamic wind and structure conditions and has therefore the potential of being more efficient than a passive solution despite its higher complexity and cost. One of the most investigated and potentially highly effective active measures to enhance the flutter performance of bridges is to endow their decks with arrays of movable flaps. The overall aim of this dissertation is to investigate, experimentally as well as theoretically, the feasibility and effectiveness of an intelligent, distributed flap system for enhancing the flutter performance of long-span bridges. The main contributions of this thesis are three-fold. First, we have designed a unique, dedicated, experimental setup consisting of a bridge section model, endowed with actively controlled flap arrays, as well as all the necessary instrumentation for measuring and perturbing the system states under controlled wind conditions, in a boundary layer wind tunnel. Secondly, we have developed an analytical model, building on top of theoretical frameworks commonly used in civil engineering for long-span bridges, and in aeronautics for wings equipped with ailerons and tabs. We have systematically evaluated the theoretical model effort with wind tunnel experiments. Thirdly, we leveraged our experimental setup and analytical model in order to thoroughly investigate different flap control coordination strategies, an unprecedented study that we are uniquely equipped for.