Mucopolysaccharidosis type IVA (MPS IVA, Morquio A syndrome) is a rare inherited disorder characterized by skeletal dysplasia due to deficient N-acetylgalactosamine-6-sulfate sulfatase activity, resulting in glycosaminoglycan (GAG) accumulation. Identifying accurate biomarkers reflecting clinical severity and therapeutic response remains challenging. This study evaluated potential surrogate biomarkers, including N-terminal pro-C-type natriuretic peptide (NT-proCNP), collagen types I and II, mono-sulfated keratan sulfate (KS), di-sulfated KS, and chondroitin-6-sulfate (C6S), in blood and urine samples from 60 patients ranging from 1 to 62 years of age. NT-proCNP levels were significantly elevated in patients of all ages and negatively correlated with growth impairment, especially after 8 years of age. Collagen type I levels significantly increased in adult patients, whereas collagen type II showed age-dependent elevations. Urinary KS, in mono- and di-sulfated forms, demonstrated moderate negative correlations with growth impairment. Moreover, NT-proCNP, mono- and di-sulfated KS in plasma, and urinary di-sulfated KS were not affected by enzyme replacement therapy in patients younger than 12 years, unlike urinary mono-sulfated KS. In conclusion, NT-proCNP has emerged as a promising independent biomarker reflecting the severity of skeletal dysplasia and possibly the near-future growth rate. These findings highlight the potential role of NT-proCNP in clinical assessment and monitoring therapeutic efficacy, addressing current unmet needs in MPS IVA management.