The present invention provides a circuit board structure having an embedded capacitor and a method for fabricating the same. The circuit board structure includes a core layer board with at least one surface having non-penetrating first and second grooves, a circuit layer and a first electrode plate formed in the first and second grooves of the core layer board respectively and being flush with the core layer board; a high dielectric material layer formed on the core layer board, the circuit layer and the first electrode plate; a second electrode plate formed on the high dielectric material layer and corresponding to the first electrode plate, thereby forming a capacitor by the first and second electrode plates and the high dielectric material layer. The high dielectric material layer is formed on a plane surface so as to eliminate poor filling and improve reliability.