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Abstract. Rationale:. A patent urachus is a rare congenital anomaly that atypically presents as an umbilical cord cyst or large umbilical cord. Here we describe a case of a giant umbilical cord cyst in a newborn diagnosed as a patent urachus. Patient concerns:. A male infant with a birth weight of 3260 g was transferred because of an antenatally diagnosed giant umbilical cord cyst accompanied by yellowish discharge and granulation in the umbilical cord after birth. Diagnoses:. Patent urachus Intervensions:. The patent urachus was treated by excision of the urachal remnant followed by partial cystectomy. Outcomes:. Postoperative orchitis with pyocele occurred and was treated with a course of antimicrobial therapy; and no other complications developed. Lessons:. Newborns with a giant umbilical cord or umbilical cord cysts should be examined for possible accompanying urachal anomalies, even if antenatal ultrasound shows no other suspicious findings, to prevent delayed diagnosis and subsequent complications.