We report a surface-enhanced Raman scattering (SERS) microchip that is capable of measuring SERS signals of liquid samples with high sensitivity. The microdevice is an integration of a silicon-based SERS substrate, a multimode optical fiber (MMF), and a microchannel embedded in the photosensitive glass fabricated by the femtosecond laser followed by thermal treatment, wet etching, and annealing. The performance of the SERS microchip is evaluated by measuring rhodamine 6G using a $632.8\mathrm{nm}$ He–Ne laser at $4.3\mathrm{mW}$ excitation power, which reveals that the detection limit is lower than ${10}^{-10}\mathrm{M}$ at a $1\mathrm{s}$ short accumulation time.