Quercetin (3,3′,4′,5,7-pentahydroxyflavone) exerts multiple pharmacological effects: anti-oxidant activity, induction of apoptosis, modulation of cell cycle, anti-mutagenesis, and anti-inflammatory effect. In topical formulations quercetin inhibits oxidative skin damage and the inflammatory processes induced by solar UV radiation. In this work, quercetin (2 mg/mL) was loaded in vesicular Penetration Enhancer containing Vesicles (PEVs), prepared using a mixture of lipids (Phospholipon® 50, P50) and one of four selected hydrophilic penetration enhancers: Transcutol® P, propylene glycol, polyethylene glycol 400, and Labrasol® at the same concentration (40% of water phase). Photon Correlation Spectroscopy results showed a mean diameter of drug loaded vesicles in the range 80–220 nm. All formulations showed a negative surface charge and incorporation efficiency in the range 48–75%. Transmission Electron Microscopy confirmed that size and morphology varied as a function of the used penetration enhancer. The influence of PEVs on ex vivo quercetin (trans)dermal delivery was evaluated using Franz-type diffusion cells, new born pig skin and Confocal Laser Scanning Microscopy. Results showed that drug delivery is affected by the penetration enhancer used in the PEVs' formulation.