This study reports a new strategy for simultaneous detection of the C-telopeptide fragments of type II collagen (CTX-II) as a biomarker of osteoarthritis (OA) using a fluoro-microbeads guiding chip. As osteoarthritis progresses, the joint components including matrix and cartilage are degraded by proteases. The degraded products such as CTX-II are released into the serum and urine, and the CTX-II concentration in body fluids reflects OA progression. Because the CTX-II has heterogeneous epitope structure in serum (sCTX-II; homodimers) and urine (uCTX-II; monomers or variant monomers), a multiple-sensing device enabling both sandwich and competitive-type immunoassays is required. For multiple assessments of serum and urinary CTX-II, we designed a fluoro-microbeads guiding chip (FMGC) containing multiple sensing areas and connecting channels. Using the approach, the sandwich (sCTX-II) and competition (uCTX-II) assays could be simultaneously performed on a single chip. We designed a fluidic control device enabling selective control of the open-close function of FMGC channels. The immune-specific signal was quantitatively analyzed by counting the number of fluorescent microbeads from the registered images. The results from the developed FMGC assay showed high correlation with those obtained in ELISA. The completion time of the FMGC assay was 24-fold and 3.5-fold shorter than the ELISA for urinary and serum CTX-II. Taken together, it enabled the simultaneous detection of both sCTX-II and uCTX-II. This FMGC-based assay would be a promising tool for monitoring of osteoarthritis.