Uncertainties regarding fission fractions are essential in understanding antineutrino flux predictions in reactor antineutrino experiments. A new Monte Carlo-based method to evaluate the covariance coefficients between isotopes is proposed. The covariance coefficients are found to vary with reactor burnup and may change from positive to negative because of balance effects in fissioning. For example, between 235U and 239Pu, the covariance coefficient changes from 0.15 to −0.13. Using the equation relating fission fraction and atomic density, consistent uncertainties in the fission fraction and covariance matrix were obtained. The antineutrino flux uncertainty is 0.55%, which does not vary with reactor burnup. The new value is about 8.3% smaller.