A 5-year-old boy with progressive muscle weakness was found to have a homozygous mutation in the FLAD1 gene (c.A554T:p.D185V in exon 2), causing lipid storage myopathy due to FAD synthetase deficiency. This mutation is associated with a severe, early-onset form of multiple acyl-CoA dehydrogenase deficiency (MADD) that is less responsive to riboflavin treatment. The case highlights the importance of FLAD1 genetic testing in patients with MADD and suggests that riboflavin therapy may provide only partial benefit for severe exon-2 mutations.