The 49XXXXY Klinefelter variant is rare and chromosomal analysis is required for diagnosis. We discuss the surgical management of incomplete penoscrotal transposition and consider this characteristic as an associated genital anomaly. We report the case of a patient who initially presented with a poor urinary stream. Physical examination revealed an incomplete penoscrotal transposition and a subcoronal hypospadias. Investigations included blood tests, abdominal Ultrasound and a chromosomal analysis. A multidisciplinary team (MDT) approach facilitated diagnosis of the 49 XXXXY Klinefelter variant. At MDT, medical and surgical management were discussed with the parent. We opted for delayed surgical correction of the incomplete penoscrotal transposition in the pre-pubertal period due to unavailability of topical hormone therapy. Operative technique aimed to relocate the scrotum in a dependent position. This was achieved via an inverted omega incision to create scrotal flaps that were rotated inferomedially for midline closure. Post-operatively, the patient can now urinate standing up with a good stream and has improved cosmesis. Incomplete penoscrotal transposition can be surgically corrected in the pre pubertal period with a good functional outcome. Chromosomal analysis is necessary in evaluating this associated genital anomaly and for diagnosis of 49XXXXY Klinefelter variant. • The 49XXXXY Klinefelter variant is rare and diagnosed by chromosomal analysis. • Incomplete penoscrotal transposition (PST) may be an associated phenotype. • Incomplete PST can be surgically corrected in the pre pubertal period.