A method of manufacturing a circuit board having waveguides including forming a waveguiding structure by injection molding. The waveguiding structure includes a plurality of waveguides arranged at intervals and at least one connecting portion connecting two adjacent waveguides. Each waveguide includes a waveguiding substrate and at least one protrusion on the waveguiding substrate. The connecting portion is removed to obtain at least two waveguides. A metal layer is formed to wrap the whole outer surface of each waveguide. A plurality of receiving grooves is formed to penetrate a wiring board. Each waveguide wrapped by the metal layer is embedded in one of the receiving grooves. The waveguides and the wiring board are fixed. A portion of the metal layer on a surface of each protrusion facing away from the waveguiding substrate is removed. A circuit board is also provided.