Over the last two decades, advances in laparoscopic surgery and minimally invasive techniques have transformed the operative management of neonatal colorectal surgery for conditions such as anorectal malformations (ARMs) and Hirschsprung’s disease. Evolution of surgical care has mainly occurred due to the use of laparoscopy, as opposed to a laparotomy, for intra-abdominal procedures and the development of trans-anal techniques. This review describes these advances and outlines the main minimally invasive techniques currently used for management of ARMs and Hirschsprung’s disease. There does still remain significant variation in the procedures used and this review aims to report the current literature comparing techniques with an emphasis on the short- and long-term clinical outcomes.