In this work, we report results from fully atomistic molecular dynamics simulations regarding the associative behavior of a third-generation poly(amidoamine) dendrimer with ibuprofen, a weakly acidic nonsteroidal anti-inflammatory drug, in aqueous solutions and at different pH conditions. Employing a combined static and dynamic approach, we describe the specifics of the complexation/encapsulation of the drug within the dendritic structure. In addition, information regarding the dynamic behavior is provided for the self- and the collective motion of the drug molecules. The detail afforded by the present molecular-level description of the relevant associative mechanisms (i.e., electrostatic complexation, hydrogen-bonding), provides a deeper insight for the interpretation of recent experimental findings regarding the behavior of dendrimer/ibuprofen systems in an aqueous environment.