Renal tubular acidosis (RTA) type 3 is a rare genetic disorder characterized by impaired bicarbonate reabsorption in the proximal renal tubules, leading to metabolic acidosis. Here, we present a case of a 6-year-old male Saudi child who was diagnosed with RTA type 3 associated with carbonic anhydrase deficiency. The patient presented with symptoms of metabolic acidosis, electrolyte abnormalities, and a family history of renal tubular acidosis. Laboratory investigations revealed metabolic acidosis, hypokalemia, and hypophosphatemia, consistent with the diagnosis of RTA type 3. Genetic testing confirmed the presence of mutations in the CA2 gene encoding carbonic anhydrase II, corroborating the diagnosis of carbonic anhydrase deficiency. The patient was managed with oral alkali supplementation and electrolyte replacement therapy to correct acidosis and restore electrolyte balance. This case underscores the importance of recognizing the rare association between RTA type 3 and carbonic anhydrase deficiency, highlighting the role of genetic testing in diagnosis and personalized management strategies for affected individuals. Further research is warranted to elucidate the underlying molecular mechanisms and optimize therapeutic interventions for this rare disorder.