A method for fabricating a circuit board structure having at least an embedded electronic element is disclosed, which includes the steps of: providing a substrate and embedding at least an electronic element in the substrate with an active surface and a plurality of electrode pads of the electronic element exposed from a surface of the substrate; forming a plurality of conductive bumps on the electrode pads of the electronic element; and covering the surface of the substrate and the active surface of the electronic element with a dielectric layer and a metal layer stacked on the dielectric layer, wherein the conductive bumps penetrate the dielectric layer so as to be in contact with the metal layer, thereby simplifying the fabrication process, reducing the fabrication cost and saving the fabrication time.