A waterproofing structure for a vehicle door having a cover member for closing a service hole formed in an inner panel, and a clip for detachably mounting the cover member to the inner panel. The cover member includes a seat portion and a tool hole. The seat portion is formed on an outer side of the cover member facing the inner panel, and the clip is mounted thereto. To detach the clip from the inner panel, a tool is inserted into the tool hole from an inner side. The clip includes a countersunk head covering the tool hole to seal the hole while the clip is mounted to the seat portion. The seat portion serves as a canopy with respect to the tool hole, and changes a course of water entering an interior of the door and falling toward the tool hole from the outer side of the cover member.