Isolated deficiency of complex II is a rare inborn error of metabolism, accounting for approximately 2% of mitochondrial diseases. Mitochondrial complex II deficiency is predominantly seen in cases with bi-allelic SDHA mutations. To our knowledge, only 11 patients and five pathogenic variants have been reported for the SDHB gene. Our patient had a severe clinical presentation with seizures and sepsis, and died at the age of 2 months. Muscle biopsy analysis was compatible with mitochondrial myopathy with complex II deficiency. The family was given a molecular diagnosis for their child 2 years after his death via a clinical exome test of a frozen muscle biopsy specimen and a novel homozygous missense variant c.592 A > G (p.Ser198Gly) in SDHB gene was detected by next-generation sequencing. Here, we present another patient with a novel homozygous SDHB variant causing severe complex II deficiency and early death.