The aim of this study was to investigate the effect of Poly(amidoamine) (PAMAM) dendrimers on corneal permeation of puerarin (PUE). Permeation studies were performed using excised cornea of rabbits by a Valia–Chien diffusion apparatus. Drug-treatment studies were carried out by measuring the penetration of puerarin on cornea in PAMAM–PUE physical mixture or PAMAM–PUE complex, and cornea-treatment studies were carried out by measuring the penetration of puerarin on PAMAM dendrimer pretreated cornea in puerarin solution. The results showed that the permeability coefficient of puerarin in PAMAM–PUE physical mixture was enhanced by 2.48 (G3), 1.99 (G4) and 1.36 (G5) times on average, respectively compared to control. However, no significant permeability enhancement of puerarin in PAMAM–PUE complex was found compared to control. This may attribute to free drug concentration was lower in PAMAM–PUE complex which served as a depot and exhibited slow-released behavior of drug. Cornea-treatment studies showed that the lag time of puerarin was decreased, while the cumulative amount within 2.5 h (Q_2.5) and the permeability coefficient of puerarin increased compared to control. The permeability coefficient of puerarin was linear correlated to the molecular weight of PAMAM dendrimer (r²=0.99). This indicates that higher generation of PAMAM dendrimer more easily interact with cornea or loosen the epithelium cell junctions than lower generation to increase the flux of puerarin. Overall, the study showed that PAMAM dendrimer increased the corneal permeation of puerarin mainly by altering the corneal barrier.