While only a few hundred cases have been reported in pediatrics, congenital glucose-galactose malabsorption (GGM) is an extremely rare autosomal-recessive metabolic disorder that is characterized by intractable diarrhea and severe dehydration, which can be life-threatening if not treated appropriately. Due to the rarity of the disease, it is challenging to consider GGM as an initial diagnosis for most clinicians. We report the clinical and diagnostic course of a seven-month-old Saudi infant who presented with severe recurrent episodes of watery diarrhea and failure to thrive in early infancy despite standard treatment. Molecular testing identified that our patient had a compound heterozygous variant in SLC5A1. Fructosebased formulae have been proven to be effective in treating GGM. This case highlights the importance of early diagnosis and timely management to prevent serious complications of undiagnosed GGM.