A circuit board structure with capacitors embedded therein and a method for fabricating the same are disclosed. The structure comprises at least two core layers individually comprising a dielectric layer having two opposite surfaces, circuit layers disposed on the outsides of the two opposite surfaces of the dielectric layer, and at least two capacitors embedded respectively on the insides of the two opposite surfaces of the dielectric layer and individually electrically connecting with the circuit layer at the same side; at least one adhesive layer disposed between the core layers to combine the core layers as a core structure; and at least one conductive through hole penetrating the core layers and the adhesive layer, and electrically connecting the circuit layers of the core layers. Accordingly, the present invention can improve the flexibility of circuit layout, and realize parallel connection between the capacitors to provide more capacitance.