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We present a framework for quantifying the uncertainty that results from the choice of exchange-correlation (XC) functional in predictions of phonon properties and thermal conductivity that use density functional theory (DFT) to calculate the atomic force constants. The energy ensemble capabilities of the BEEF-vdW XC functional are first applied to determine an ensemble of interatomic force constants, which are then used as inputs to lattice dynamics calculations and a solution of the Boltzmann transport equation. The framework is applied to isotopically-pure silicon. We find that the uncertainty estimates bound property predictions (e.g., phonon dispersions, specific heat, thermal conductivity) from other XC functionals and experiments. We distinguish between properties that are correlated with the predicted thermal conductivity [e.g., the transverse acoustic branch sound speed ($R^2=0.89$) and average Grüneisen parameter ($R^2=0.85$)] and those that are not [e.g., longitudinal acoustic branch sound speed ($R^2=0.23$) and specific heat ($R^2=0.00$)]. We find that differences in ensemble predictions of thermal conductivity are correlated with the behavior of phonons with mean free paths between $100$ and $300$ nm. The framework systematically accounts for XC uncertainty in phonon calculations and should be used whenever it is suspected that the choice of XC functional is influencing physical interpretations.