Cleft lip and palate (CLP) are one of the most frequently occurring craniofacial congenital anomalies. A syndromic association is frequently seen in such cases. A feeding obturator is a prosthetic aid that assists a patient in obturating a cleft until surgery is performed. Cleft lip surgery or cheiloplasty is often performed three months after birth, while palate surgery or palatoplasty is typically performed between the ages of six and fourteen months. A 2-day-old newborn presented to the Pediatric Emergency with a complaint of difficulty in feeding. On examination, bilateral cleft of the lip and unilateral cleft of the palate was present. The ultrasonography of the fetus before the birth had revealed non-visualized left kidney, so an ultrasonography (USG) of the abdomen and pelvis was advised which confirmed the finding i.e., left renal agenesis. Electrocardiography (ECG) revealed an arterial septal defect (ASD) of 4.5 mm. Such presentation is commonly seen in cases of isolated gonadotropin-releasing hormone (GnRH) deficiency (IGD). A custom-made feeding obturator was fabricated and delivered to help the baby overcome feeding difficulties. Parents were instructed and well-taught to feed the child with the appliance in place. Apart from giving appropriate instructions regarding feeding and maintenance of the appliance, parents were also informed about the surgical procedures that would be followed at a later date. Also, considering the exceptional psychological situation of the family and the need for a long-standing relationship between the cleft team for a successful outcome, appropriate counseling with reassurance was rendered to the family members.