We present a novel microfluidic surface-enhanced Raman scattering (SERS) sensor for rapid and label-free biomolecular detection. Our sensor design mitigates a common limiting factor in microfluidic SERS sensors that utilize integrated nanostructures: low-efficiency transport of biomolecules to nanostructured surface which adversely impacts sensitivity. Our strategy is to increase the total usable nanostructured surface area, which provides more adsorption sites for biomolecules. Specifically, nanoporous gold disk (NPGD) array, a highly effective SERS substrate, has been monolithically integrated inside a microfluidic chip. Individual NPGD is known to feature an order of magnitude larger surface area than its projected disk area. The increased surface area arises from nanoscale pores and ligaments 3- dimensionally distributed in the NPGD, which manifest themselves as high-density SERS hot-spots. High-density NPGD arrays further guarantee large coverage of these hot-spots on the microchannel floor. The SERS-active NPGD arrays enable highly-reproducible SERS measurements with relative intensity variations from 8% to -8%. R6G solutions in the concentrations ranging from 1 μM to 1 mM have been detected and quantitatively evaluated, and the performance of the sensor in continuous-flow condition has been assessed. Moreover, the sensor’s capabilities have been studied by detecting and identifying a physiological metabolite (urea), and the results show lower detection limit compared to best results from most recent work using integrated nanostructured surface inside microchannels. We expect that the sensor would be applicable for detecting, identifying and quantifying molecules for some point-of-care applications, i.e. urine screening.