α-(3-(1-Pyridinio)-propyl)-polydimethylsiloxane iodide (PDMS-Py+I−) and α-(3-(N,N-dimethylethylammonio)-propyl)polydimethylsiloxane iodide (PDMS-Am+I−) were prepared from PDMS containing iodopropyl group at the chain end. The prepolymer was synthesized by a ring-opening polymerization of hexamethylcyclotrisiloxane (D3) initiated with lithium trimethylsilanolate followed by the termination with 3-chloropropyldimethylchlorosilane and the halogen substitution with sodium iodide. All the polymers effectively enhanced the drug penetration through the skin and the permeation coefficients were about 2–6 times as much as that without enhancer. It was revealed from the detailed analysis of the permeation profile that the permeation and partition coefficients increased in parallel, with increasing of the average degree of polymerization, while the diffusion coefficients were unchanged.