Palatal fistula is a challenging complication following cleft palate repair. We investigated the usefulness of collagen matrix in the prevention of postoperative fistula. We performed a retrospective cohort study of patients with cleft palate who underwent primary palatoplasty (Furlow's double opposing z-plasty) in Seoul National University Children's Hospital. Collagen Graft and Collagen Membrane (Genoss, Suwon, Republic of Korea) were selectively used in patients who failed complete two-layer closure. The effect of collagen matrix on fistula formation was evaluated according to palatal ratio (cleft width to total palatal width) and cleft width. A total of 244 patients (male, 92 and female, 152; median age, 18 months) were analyzed. The average cleft width was 7.0 mm, and the average palatal ratio was 0.21. The overall fistula rate was 3.6% (9/244). Palatal ratio (p = 0.014) and cleft width (p = 0.004) were independent factors impacting the incidence of postoperative fistula. Receiver operating characteristic curve analysis showed that the cutoff values in terms of screening for developing postoperative fistula were a palatal ratio of 0.285 and a cleft width of 9.25 mm. Among nonsyndromic patients with values above those cutoffs, the rates of fistula development were 0/5, 1/6 (16.7%), and 4/22 (18.2%) for those who received Collagen Graft, Collagen Membrane, and no collagen, respectively. Collagen matrix may serve as an effective tool for the prevention of palatal fistula when complete two-layer closure fails, especially in wide palatal clefts. The benefit was most evident in Collagen Graft with thick and porous structure.