This paper aims to highlight the possible surgical steps that could affect the neural supply of soft palate and velopharyngeal sphincter during Furlow palatoplasty and posteriorly-based myo-mucosal buccal flaps in patients with persistent velopharyngeal insufficiency after primary cleft palate repair. Non-syndromic patients with persistent hypernasality (after primary cleft palate repair) who had Furlow palatoplasty or posteriorly-based buccal myo-mucosal flaps and were followed up for at least 60 months after the secondary surgery. All patients were examined using a fiberoptic endoscopy, the movement of components of the velopharyngeal sphincter: soft palate, and lateral pharyngeal walls were traced on the monitor and given a score from 0–4. Patients’ characteristics, auditory perceptual assessment, the severity of hypernasality, intraoperative lengthening of the palate, and operative complications were recorded. At postoperative (at least 60 months) evaluation of the patients statistically non-significant differences were reported when comparing the pre-versus post-operative auditory perceptual assessment following both procedures (P value ≥0.05). A greater tendency towards improvement was noticed with BF but was non-significant. The nerve supply of the palate could be jeopardized by many techniques of primary or secondary repair of the cleft palate leaving behind a deceiving intact but weak poor-functioning palate. All efforts should be made to provide more neural-preservation techniques in primary/secondary repair of the cleft palate. Further wide-scale research is essential to have final clear conclusions.