The standard lore in noncommutative physics is the use of first order variational description of a dynamical system to probe the space noncommutativity and its consequences in the dynamics in phase space. As the ultimate goal is to understand the inherent space noncommutativity we propose a variational principle for noncommutative dynamical systems in configuration space, based on results of our previous work [14]. We hope that this variational formulation in configuration space can be of help to elucidate the definition of some global and dynamical properties of classical and quantum noncommutative space.