A flexible printed circuit board with waterproof structure includes a flexible substrate that has a first surface having a first metal layer bonded thereon. The first metal layer forms a covered area and at least one mounting zone. A bonding strength enhancing structure is formed on the mounting zone. A first insulation layer is formed on the covered area of the upper surface of the first metal layer in such a way to expose the mounting zone. A water resistant member is bonded to the bonding strength enhancing structure and a second surface of the flexible substrate.