Background Aphallia is a rarest of rare congenital anomaly the incidence being 1 in 10 to 30 million live births. Seen at birth, it leaves the parents and family disturbed. Immediate counselling though done; it may take time for the parents to come to a decision. Case presentation A newborn was brought for genital examination and since the penis was not present and the scrotum with testes were normal, aphallia was suspected. At 1 month after all the necessary investigations, isolated aphallia without any other congenital anomalies was confirmed. The options offered were gender reassignment before the age of 18 months or staged phallo and urethroplasty. Parents are so far undecided. Conclusions Aphallia results from failure of the genital tubercle to develop, leading to the absence of all the penile components. Diagnosis of aphallia includes the absence of the phallus, male karyotype and normally developed scrotum with normal testicles. Usually, this anomaly is associated with multiple other anomalies involving the urinary, gastrointestinal and musculoskeletal systems. Management of this condition is challenging and requires a multidisciplinary approach. In addition to managing the associated anomalies, the options to treat aphallia will depend on the type, severity of associated anomalies, family background and socioeconomic status of the family. Psychological counselling along with surgery (in the form of gender reassignment or phalloplasty) are the mainstays of treatment. The literature of this anomaly and the treatment is reviewed.