The lipid bilayer bending modulus, characterized by thermal undulations, is often affected by the presence of membrane active molecules. However, complex interplay between headgroup charges, hydration, and bilayer structural parameters such as bilayer thickness make it difficult to understand the changes in bending modulus. Using neutron spin-echo measurements, the effect of ibuprofen, a model nonsteroidal anti-inflammatory drug, on the bending modulus of phospholipid membranes is studied as a function of pH and temperature. Ibuprofen was found to lower the bending modulus at all pH values. We present molecular insights into the observed effect on membrane dynamics based on molecular dynamics simulations and small-angle neutron scattering based structural perturbations as well as changes in zwitterionic headgroup electrostatics due to pH and addition of ibuprofen.