A 15-year-old boy experienced painless vision loss in the left eye of unknown duration. Leber hereditary optic neuropathy (LHON) was suspected, despite negative testing for the 3 most common pathogenic gene mutations and idebenone 300 mg 3 times daily was prescribed. Nine months later, the patient developed right eye involvement. Complete mitochondrial genome analysis revealed 2 rare variants - m.3890G>A of the MT-ND1 gene and m.8417C>A of the MT-ATP8 gene. The former has been described in severe infantile Leigh syndrome and LHON; the latter is of unknown significance. The patient experienced progressive visual deterioration through 12 months, but improved to 20/20, right eye and 20/25, left eye, at 21 months. Visual recovery can occur in a patient with bilateral optic neuropathy secondary to the rare m.3890G>A point mutation.