Recently, three successful antineutrino experiments (Daya Bay, Double Chooz, and RENO) measured the neutrino mixing angle θ 13 ; however, significant discrepancies were found, both in the absolute flux and spectral shape. Much effort has been expended investigating the possible reasons for the discrepancies. In this study, Monte Carlo-based sampling was used to evaluate the fission fraction uncertainties. We found that fission cross-section uncertainties are an important source of uncertainty for 235 U, 239 Pu, and 241 Pu, but for 238 U, elastic and inelastic cross-sections are more important. Among uncertainty related to manufacturing parameters, fuel density is the main uncertainty; however, the total manufacturing uncertainty was very small. The uncertainties induced by burnup were evaluated through the atomic density uncertainty of the four isotopes. The total fission fraction uncertainties from reactor simulation were 0.83%, 2.24%, 1.79%, and 2.59% for 235 U, 238 U, 239 Pu, and 241 Pu, respectively, at the middle of the fuel cycle. The total fission fraction uncertainty was smaller than the previously derived value of 5%. These results are helpful for studying the reactor antineutrino anomaly and precisely measuring the antineutrino spectrum in the Daya Bay antineutrino experiment.