Pfeiffer syndrome is a rare genetic condition that includes anomalies of the head, hands, and feet. It was originally described by Rudolf Pfeiffer in 1964. As a result of varied clinical presentations, there is a low threshold for missing the diagnosis. Three (3) cases were found by the authors in the medical literature from the African continent, all of which lacked molecular studies. The main dysmorphic features we observed in our patient were; macrocephaly with widely gaped sagittal sutures, proptosis with ocular hypertelorism, ankylosed elbows, wide sandal gap and medially deviated broad great toes. In this case, sequence analysis using Illumina technology and deletion/duplication testing of 65 genes for variants associated with craniosynostosis syndromes was performed at Invitae Medical Genetic laboratory. A diagnosis of Pfeiffer syndrome type 3 with FGFR2 c.1052C>G (p.Ser351Cys) variant was made. In conclusion, this case will aid health care providers especially in areas of low accessibility to molecular studies to promptly identify, appropriately manage the condition as well as counselling the parents to offset the risk of abandonment of neonates with dysmorphic features.