Townes-Brocks syndrome is a rare autosomal dominant syndrome characterized by multiple malformations, including thumb anomalies. Thumb hypoplasia poses a specific problem, where a deficient thumb creates a significant handicap in hand function. The treatment goal is enabling pinch and grip activity, and the preferred procedure for a severely hypoplastic thumb is index finger pollicization. We present a case of on-top index pollicization in a 10-year-old, after a partial amputation of a previously syndactylized hypoplastic thumb, with a well-formed first carpometacarpal joint. The decision to proceed with pollicization was made after considering second toe-to-hand transfer and a standard pollicization with an amputation of the thumb remnants. Six months after the procedure, the outcome was evaluated as “good” (19 points) with Percival's assessment method. The patient uses the operated hand in all activities of daily life and is doing well in school. This patient's diagnosis of Townes-Brocks syndrome was confirmed with genetic testing, which gives grounds and incentive to further investigate other possible related conditions, and provide genetic counselling and risk assessment. In reconstruction of complex thumb malformations, especially after previous multiple operations, an individually tailored reconstruction plan, sometimes involving modifications of standard reconstructive procedures, is paramount in achieving good results.