Chondroitin sulfate (CS) is a sulfated polysaccharide produced by chondrocytes. Alkaline phosphatase (ALP) is an important enzyme involved in the mineralization of chondrocytes. In recent years, it has been reported that CS regulates the differentiation of various cells. In this study, we investigated the effect of supplemented CS on ALP activity and mineralization of the chondrogenic cell line, ATDC5. In addition, hyaluronic acid (HA), a non-sulfated and acidic polysaccharide, was used in comparison to CS. CS and HA significantly suppressed ALP activity without affecting ATDC5 cell proliferation. In addition, although the inhibition of ALP activity was observed at every time point, Alp mRNA expression level was not affected by CS. The suppressive effect of CS on ALP activity was abrogated by pre-treatment with chondroitinase ABC (CSase). CS and L-homoarginine (hArg), an inhibitor of ALP, significantly suppressed mineralization in ATDC5 cells. In conclusion, supplemented CS directly inhibits ALP to prevent the progression of chondrocytes from differentiation to mineralization.