A method for manufacturing a circuit board structure with a waveguide is provided. The method includes: providing a first substrate unit, a second substrate unit, a third substrate unit, and two adhesive layers, the first substrate unit including a first dielectric layer and a first conductive layer, the first conductive layer including a first shielding area and two first artificial magnetic conductor areas disposed on two sides of the first shielding area; the second substrate unit including a second dielectric layer and a second conductive layer, the second conductive layer including a second shielding area; the third substrate unit defining a first slot, and the adhesive layer defining a second slot; stacking the first substrate unit, one of the adhesive layers, the third substrate unit, another one of the adhesive layers, and the second substrate unit in that order; pressing the intermediate body.