Bladder exstrophy-epispadias complex (BEEC) is a rare congenital condition with a global prevalence of 2–8 cases per 100,000 newborns. It predominantly affects males and is associated with risk factors such as low birth weight, Caucasian ethnicity, maternal smoking, and family history. The etiology is multifaceted, with the “wedge effect” and pelvic ring malrotation theories suggesting anatomical disruptions during embryogenesis. The most critical embryological structures and events involved include the cloacal membrane, the timing of its rupture, the presence or absence of a urorectal septum, and an abnormal migration of mesenchymal cells. Molecularly, the sonic hedgehog (SHH) signaling pathway and the p63 gene are implicated, with disruptions potentially contributing to BEEC. Recent studies have also pointed toward the role of other genes and pathways, including the BMP4 pathway and the ISL1 gene, in the pathogenesis of BEEC. Despite these insights, the precise pathophysiology remains elusive, necessitating further research for improved management and potential prevention strategies. This underscores the need for continued exploration into the genetic and molecular underpinnings of BEEC to fully understand its etiology and develop effective therapeutic strategies.