A waterproof electronic packaging structure includes a carrier plate, a chip, an encapsulating member and a waterproof member. The carrier plate includes a substrate, and a leadframe partly embedded in the substrate and including a chip bonding portion exposed from the substrate. The chip is mounted to the substrate and is electrically connected to the chip bonding portion. The encapsulating member is formed on the carrier plate, and encapsulates the chip and the chip bonding portion. The waterproof member is formed on the encapsulating member, and covers an outer surface of the encapsulating member and an interface between the encapsulating member and the substrate. A method for making a waterproof electronic packaging structure is also disclosed.