A rail fastener sealing system comprises a dowel having a substantially cylindrical elongated body and a dowel passage configured to receive a fastener that secures a rail to a rail tie. The sealing system further includes a seal positioned on an end of the dowel. The seal includes a flexible body having a central passage extending through the flexible body and a lip extending circumferentially around an opening of the central passage. The lip of the seal is disposed adjacent the end of the dowel and at least a portion of the flexible body of the seal is positioned within the dowel passage.