The aim of this work was to investigate the effect of backing films on transdermal delivery of donepezil (DP) from patches. Three backing films, Cotran™ 9700, Cotran™ 9701, and Cotran™ 9726 were chosen as backing layers to prepare transdermal patches containing DP. The transdermal penetration and release amount of DP from each patch were evaluated by rabbit abdominal skin in vitro. The partitioning experiments and attentuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy were performed to confirm the existence of interaction between backing films and DP. Results showed that the cumulative release amount of DP from patches with different backing films had the same order of cumulative amount penetrated, i.e. Cotran™ 9701 < Cotran™ 9700 < Cotran™ 9726, which demonstrated that the permeation of DP was mainly limited by release behavior. Partitioning experiments and ATR-FTIR study indicated that Cotran™ 9700 and Cotran™ 9701 had interaction with DP by H bond formation which decreased the release of drug from the patches. By contrast, Cotran™ 9726 could provide the highest flux of skin permeation of DP, because such interaction between them was not found. Moreover, the parameters of backing films were found to have relation to skin hydration, thus affecting the penetration behavior of DP from patches. In conclusion, the effect of backing films on the flux of DP permeation could be attributed to both the interaction of backing films and the changes of skin hydration. Backing films could be a key factor in formulation screening of DP patches.