This case report describes the retinal optical coherence tomography (OCT) findings in a microcephalic infant with macular atrophy presumably caused by intrauterine Zika virus infection. OCT demonstrated atrophy of the outer retinal layers and choriocapillaris, including the outer nuclear layer and ellipsoid zone, associated with retinal pigment epithelium hyper-reflectivity and increased OCT penetration into deeper layers of the choroid and sclera. A major concern associated with this infection is the apparent increased incidence of microcephaly in fetuses born to mothers infected with the Zika virus. It is becoming increasingly difficult to ignore the upsurge in congenital microcephaly observed in Brazil. Recently, ocular findings in infants with microcephaly associated with intrauterine Zika virus infection have been described. This is the first report of OCT imaging of macular atrophy in a child with presumed Zika virus infection-associated microcephaly.