Mitochondrial trifunctional protein (MTP) is a multienzyme complex involved in the metabolism of long-chain hydroxyacyl-CoA, a product of the fatty acid β-oxidation cycle. MTP is an α4β4 hetero-octomer encoded by two different genes: HADHA (OMIM 600890) and HADHB (OMIM 143450). MTP deficiency induces three different types of presentation: (1) a lethal phenotype with neonatal onset (severe); (2) a hepatic phenotype with infant onset (intermediate); and (3) a neuromyopathic phenotype with late-adolescent onset (mild). While acylcarnitine analysis has revealed increased levels of long-chain hydroxyacylcarnitine in blood when an MTP deficiency exists, the neuromyopathic type is usually asymptomatic and does not always result in an abnormality in acylcarnitine analysis results. We report here the case of a 13-year-old girl with recurrences of intermittent myalgia since her early childhood, for whom the disorder had not been definitely diagnosed. Since she was referred to our hospital because of rhabdomyolysis, we have repeatedly performed blood acylcarnitine analysis and found slight increases in long-chain 3-OH-acylcarnitine levels, on the basis of which we made a chemical diagnosis of MTP deficiency. Immunoblot analysis of skin fibroblasts revealed loss of α- and β-subunits of MTP. In addition, analysis of the HADHB gene, which encodes long-chain 3-ketoacyl-CoA thiolase, one of the enzymes constituting MTP, identified compound heterozygous mutations of c.520C>T (p.R141C) and c.1331G>A (p.R411K). MTP deficiency is considered an extremely rare disorder, as only five cases (lethal phenotype, two patients; hepatic phenotype, two patients; and neuromyopathic phenotype, one patient) have thus far been reported in Japan. However, it is likely that the neuromyopathic phenotype of MTP deficiency has not yet been diagnosed among patients with recurrences of intermittent myalgia and rhabdomyolysis, as in our patient reported here.