Background: Mitochondrial depletion syndrome (MDS) is phenotypically heterogeneous and may affect either single or multiple organs including muscles, liver, brain, and kidneys. FBXL4-related mitochondrial depletion syndrome of encephalomyopathic type is a severe condition that begins at an early age. It is primarily linked to brain dysfunction combined with muscle weakness. Case presentation: In the present case, a homozygous loss of function variant of FBXL4 (MIM 605654) was identified by whole exome sequencing (WES) in a three-year old Saudi girl who exhibited biochemical, and cerebral magnetic resonance imaging features consistent with mitochondrial DNA depletion syndrome 13, but had different presentations which has not been reported before. Conclusion: MDTP13 (encephalomyopathic type) is caused by biallelic pathogenic variants in FBXL4. There is remarkable variability in genotypeto-phenotype correlation characteristic of this disease.