Abstract Objectives Aromatase deficiency is a rare autosomal recessive condition due to a mutation in the CYP19A1 encoding aromatase enzyme. This enzyme protects the fetus and mother from excess androgens by converting them into estrogen. We are reporting a case of aromatase deficiency presented with atypical genitalia and maternal virilization due to a novel mutation in CYP19A1. Case presentation A 10-day-old newborn presented with atypical genitalia and a history of maternal virilization during pregnancy. On examination, the baby had a Prader score of 3. Further investigation revealed karyotype 46 XX, with a normal uterus and ovaries on ultrasonography. The hormonal profile of the baby was normal except for the raised follicle stimulating hormone (FSH). Maternal ultrasound revealed polycystic ovaries, and the hormonal profile was within the normal range with slightly raised testosterone. Whole exome sequencing was done, which reported that the baby was carrying a novel homozygous mutation of the CYP19A1 gene c.575G>C p. (Arg192Pro), confirming the diagnosis of aromatase deficiency. Conclusions Aromatase deficiency is a rare condition. A history of maternal virilization during pregnancy in a child born with atypical genitalia should alert physicians to consider aromatase deficiency.