3-Hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase deficiency is an autosomal recessive disorder involving ketone body synthesis and leucine degradation. It is characterized by vomiting, hypotension, lethargy, metabolic acidosis, and non-ketotic hypoglycemia. A 3-month-old girl presented with clinical symptoms of vomiting and drowsiness. Her clinical findings included hypoglycemia, hyperammonemia, metabolic acidosis, and elevated alanine aminotransferase and aspartate aminotransferase levels. The level of C5OH acylcarnitine was elevated as determined by liquid chromatography–tandem mass spectrometry. The levels of 3-methylglutaric acid, 3-methylglutaconic acid, 3-OH isovaleric acid, glutaric acid, and 3-hydroxy-3-methylglutaric acid were found to be elevated in the analysis of urinary organic acids. According to these clinical and laboratory findings, she was diagnosed with HMG-CoA lyase deficiency. Carnitine treatment and protein- and fat-restricted and carbohydrate-rich diet were started. HMG-CoA lyase deficiency is one of the disorders that should be considered in the presence of non-ketotic hypoglycemia, metabolic acidosis, and hyperammonemia.