Background Biallelic pathogenic variants in SLC5A6 resulting in sodium‐dependent multivitamin transporter (SMVT) defect have recently been described as a vitamin‐responsive inborn error of metabolism mimicking biotinidase deficiency. To our knowledge, only 16 patients have been reported so far with various clinical phenotypes such as neuropathy and other neurologic impairments, gastro‐intestinal dysfunction and failure to thrive, osteopenia, immunodeficiency, metabolic acidosis, hypoglycemia, and recently severe cardiac symptoms. Methods We describe a case report of a 5‐month‐old girl presenting two recurrent episodes of metabolic decompensation and massive cardiac failure in the course of an infectious disease. We compare clinical, biological, and genetic findings of this patient to previous literature collected from Pubmed database (keywords: Sodium‐dependent multivitamin transporter (SMVT), SMVT defect/disorder/deficiency, SLC5A6 gene/mutation). Results We highlight the life‐threatening presentation of this disease, the stagnation of psychomotor development, the severe and persistent hypogammaglobulinemia, and additionally, the successful clinical response on early vitamin supplementation (biotin 15 mg a day and pantothenic acid 100 mg a day). Metabolic assessment showed a persistent increase of urinary 3‐hydroxyisovaleric acid (3‐HIA) as previously reported in this disease in literature. Conclusion SMVT deficiency is a vitamin‐responsive inborn error of metabolism that can lead to a wide range of symptoms. Increased and isolated excretion of urinary 3‐hydroxyisovaleric acid may suggest, in the absence of markedly reduced biotinidase activity, a SMVT deficiency. Prompt supplementation with high doses of biotin and pantothenic acid should be initiated while awaiting results of SLC5A6 sequencing as this condition may be life‐threatening. We highlight the life‐threatening presentation of SMVT deficiency. Increased and isolated excretion of urinary 3‐hydroxyisovaleric acid may suggest, in the absence of markedly reduced biotinidase activity, a SMVT deficiency. Prompt supplementation with high doses of biotin and pantothenic acid should be initiated while awaiting results of SLC5A6 sequencing as this condition may be life‐threatening and a high dose of these water‐soluble vitamins seems harmless.