TheARR3gene, also known as cone arrestin, belongs to the arrestin family and is expressed in cone cells, inactivating phosphorylated-opsins and preventing cone signals. Variants ofARR3reportedly cause X-linked dominant female-limited early-onset (age < 7 years old) high myopia (< − 6D). Here, we reveal a new mutation (c.228T>A, p.Tyr76*) inARR3gene that can cause early-onset high myopia (eoHM) limited to female carriers. Protan/deutan color vision defects were also found in family members, affecting both genders. Using ten years of clinical follow-up data, we identified gradually worsening cone dysfunction/color vision as a key feature among affected individuals. We present a hypothesis that higher visual contrast due to the mosaic of mutatedARR3expression in cones contributes to the development of myopia in female carriers.