© 2021, Springer-Verlag GmbH Germany, part of Springer Nature.Urorectal septum malformation sequence (URSM) is a rare congenital anomaly of caudal end of mesoderm. There is usually a single or no opening in the perineum. An infant with dysmorphic facial features, ambiguous genitalia, meningomyelocele, pes equinovarus, left renal agenesis, severe hydronephrosis of the right kidney, and anuria requiring right ureterocutaneostomy during the neonatal period is reported. Initial physical examination revealed fusion of labioscrotal folds forming a single sac without a raphe, and a single gonad on the left side of the sac, less than 1 mm in size. There was no phallus, urethral opening, or any palpable cavernous body. Karyotype analysis from peripheral blood was 46XY. Chromosomal microarray analysis using Agilent 8X60K platform revealed arr [hg19](1-22)x2,(X,Y)x1. DNA sequence analysis for WT1 gene was normal. During inguinal hernia repair, cavernous bodies were detected in the retroperitoneal space under the hernia sac intraoperatively. Penis was reconstructed using two rotational flaps from the midline skin above the pubic bone to cover the cavernous bodies. This report aims to discuss the clinical features as well as surgical options for reconstruction of an abnormally located penis in an infant with partial URSM. Level of evidence: Level V, therapeutic study.