Complement Factor I (CFI) deficiency, an autosomal recessive immunodeficiency disorder, presents challenges in diagnosis and management due to its rarity and varied clinical manifestations. We report the case of a 44-year-old patient with compound heterozygous CFI deficiency, a rare presentation characterized by impaired complement system regulation. The patient exhibited a history of recurrent respiratory infections and two episodes of meningococcal meningitis. Laboratory analyses revealed low complement levels and genetic testing identified two heterozygous mutations in the CFI gene. Notably, the patient also had a partial deficiency in complement component C2. Despite detectable factor I levels, the patient’s immune function remained compromised, emphasizing the complexity of CFI deficiency. Our findings underscore the importance of comprehensive complement studies and genetic analysis in diagnosing rare immunodeficiency diseases. Further research and collaboration are needed to better characterize and develop treatments for CFI deficiency and related disorders.