The Annular Core Research Reactor (ACRR) Monte Carlo N-Particle (MCNP) model is used by ACRR reactor operators and experiment designers at Sandia National Laboratories for a variety of computational calculations ranging from reactor kinetics parameter estimates and safety analyses to experimental planning. To understand the dominant source of uncertainty within the MCNP model, perturbations in temperature were applied to individual ACRR MCNP fuel rods. Fuel rod temperatures were randomly sampled from a uniform distribution from operational temperatures to quantify temperature-related uncertainty effects. Stochastic mixing was used to blend the cross sections of the desired temperatures using the MCNP continuous and Thermal Neutron Scattering Treatment [S(α,β)] libraries in ENDF/B-VII.1. This uncertainty analysis produced a 640 row × 640 column correlation and covariance matrix of the neutron energy spectra. Positive covariance was produced around the 1-MeV region and the 0.2-eV region. Correlation was found in the thermal and fast energy regions, but no correlation was observed in the slowing-down energy region because interactions in this region are not dominated by fuel.