A palatal fistula is an adverse outcome of cleft palate repair. It is unknown if a palatal fistula will influence velopharyngeal closure, even after repair of the fistula. This study determines the effect of a soft palate fistula on the risk of developing velopharyngeal insufficiency. A retrospective chart review was conducted on patients who underwent primary cleft palate repair between 2000 and 2015, with complete records at 4 years of age. Fistulae involving the secondary palate following primary palatoplasty were classified as the soft or hard palate. A forced-entry multivariate logistic regression model was built to detect predictors of velopharyngeal dysfunction. Records of 329 patients were analyzed with a mean follow-up of 8.7 years. A palatal fistula was identified in 89/329 patients (27%) and 29/329 patients (9%) underwent an independent fistula repair. Of the patients with fistula, 44% were located in the hard palate only and 56% had soft palate involvement. Compared to patients without a fistula, rates of velopharyngeal dysfunction were significantly higher in patients with a fistula involving the soft palate (OR 3.875, CI: 1.964-7.648, P < .001) but not in patients with a hard palate fistula (OR 1.140, CI: 0.497-2.613, P = .757). Veau class, age at primary repair, and syndromic status were not significant predictors of VPI (0.128≤P ≤ .975). A palatal fistula involving the soft palate is a significant predictor for development of velopharyngeal dysfunction after primary palatoplasty. Surgical intervention, at the time of fistula repair, to add vascularized tissue may be indicated to prophylactically decrease the risk of velopharyngeal dysfunction.