Binary mixtures of ethanol and phospholipids DOPC and DOPE have been investigated in a composition range relevant for topical drug delivery applications. This was done using a combined computer simulation and experimental approach where molecular dynamics simulations of ethanol–lipid mixtures with different compositions were performed. Several key properties including diffusion coefficients, longitudinal relaxation times, and shear viscosity were computed. In addition, diffusion coefficients, viscosities and NMR longitudinal relaxation times were measured experimentally for comparison and in order to validate the results from simulation. Diffusion coefficients and relaxation times obtained from simulations are in good agreement with results from NMR and computed viscosities are in reasonable agreement with viscometry experiments indicating that the simulations provide a realistic description of the ethanol–phospholipid mixtures. Structural changes in the simulated systems were investigated using an analysis based on radial distribution functions. This showed that the structure of ethanol–DOPC mixtures remains essentially unchanged in the investigated concentration range while ethanol–DOPE mixtures undergo structural rearrangements with the tendency for forming small aggregates on the 100 ns time scale consisting of less than 10 lipids. Although our simulations and experiments indicate that no larger aggregates form, they also show that DOPE has stronger aggregation tendency than DOPC. This highlights the importance of the character of the lipid headgroup for lipid aggregation in ethanol and gives new insights into phase equilibrium, dynamics and rheology that could be valuable for the development of advanced topical drug delivery formulations.