We present a unique case of umbilical cord cysts of allantoic and omphalomesenteric remnants with progressive cord edema during pregnancy. Enlargement of the umbilical cord was observed initially at 28 weeks’ gestation; the cord cysts were first recognized at 17 weeks. At 37 weeks, a cesarean section was performed and a male infant weighing 2,300 g was delivered. The entire length of the umbilical cord was 80 cm; the 50-cm proximal portion was strikingly edematous and was 7 cm in diameter. On the 1st day of life, operative exploration was undertaken via an infraumbilical incision. It was evident that a patent urachus protruded from the bladder. The lesion was excised and the bladder was closed in a two-layer anastomosis. Histologically, the intestinal epithelium was connected to the transitional epithelium at the top of the urachus, indicating allantoic remnants fused with omphalomesenteric remnants. Such a case has not been reported previously. It was considered that the overflow of urine from allantoic remnants to omphalomesenteric remnants caused the extraordinary edema of the umbilical matrix. Based on our experience, finding progressive umbilical cord edema may indicate a patent urachus co-existing with allantoic and omphalomesenteric remnants.