A 9-year-old girl developed steroid-resistant nephrotic syndrome (SRNS), in which a renal biopsy revealed focal segmental glomerulosclerosis. The girl had only a partial response to treatment with tacrolimus, lisinopril and losartan. Whole exome sequencing identified two heterozygous variants in the COQ2 gene: a known paternally inherited pathogenic variant c.683A>G and a novel maternally inherited splice site variant c.692+3A>G, classified as a variant of undetermined significance (VUS). The c.683A>G variant is typically associated with severe, early-onset disease, but the patient had relatively late-onset with isolated nephropathy. Coenzyme Q10 (CoQ10) is a component of the mitochondrial electron transport chain, its deficiency caused by mutations in COQ2 can lead to SRNS, which responds to CoQ10 supplementation. A rapid genetic diagnosis enabled treatment with high doses of ubiquinone (30 mg/kg/day) to be started, which brought significant clinical improvement and prevented further deterioration of renal function.