Surfactant protein C (SP-C) is a hydrophobic lipoprotein necessary for lowering alveolar surface tension and lung defense mechanisms. Defects in its function due to genetic mutations in the SFTPC gene have been increasingly identified in patients presenting with childhood interstitial lung disease. SFTPC mutations are inherited in an autosomal dominant pattern with reduced penetration and variable expressivity, although de novo mutations have also been documented. In this article, we present the case of an oxygen-dependent 13-year-old male with interstitial lung disease and severe pulmonary hypertension. Genetic analysis and lung biopsy confirmed the diagnosis of SP-C deficiency with the rare heterozygous mutation IVS4+2. To our knowledge, this is the first documented case of SP-C deficiency in the Puerto Rican population and the second worldwide with the IVS4+2 genetic mutation.