To describe a comprehensive decision-making process for surgical correction of structural Velopharyngeal Dysfunction (VPD) following cleft palate repair and evaluate its efficacy. Retrospective study. Tertiary care hospital. 300 consecutive patients with unilateral or bilateral cleft lip and palate (CLP) or isolated cleft palate (CP) diagnosed with clinical VPD following cleft palate repair between 2009 and 2014. Of these 206 patients had structural VPD and underwent surgical correction. Surgical corrections were carried out according to the comprehensive two stage decision making process developed by the investigators. Step 1 of decision-making involved visualisation of the VP sphincter function by nasoendoscopy. This was followed by step 2 which involved per-operative identification of scarring, tissue loss, hypoplasia and other structural deficiencies in the soft palate and septal mucoperiosteum. The choice of operation was then made from a repertoire of interrelated and escalating surgical procedures consisting of palate revision and pharyngoplasties ranging from most anatomical to the least. Evidence of postoperative restoration of VP function on nasoendoscopy, evaluation of speech for hypernasality, understandability, acceptability and symptoms of obstructive sleep apnea. Complete VP closure was demonstrated in 94% of patients treated using this algorithm. There was significant improvement in all speech parameters (p < 0.00001). Our comprehensive decision-making process is designed to effectively correct structural VPD according to the severity of structural and functional deficiencies in the soft palate and avoid over treatment.