We compute the contribution of phonons to the thermal conductivity in the core of superfluid neutron stars. We use effective field theory techniques to extract the phonon scattering rates, written as a function of the equation of state of the system. We also calculate the phonon dispersion law beyond linear order, which depends on the gap of superfluid neutron matter. With all these ingredients, we solve the Boltzmann equation numerically using a variational approach. We find that the thermal conductivity κ is dominated by combined small and large angle binary collisions. As in the color-flavor-locked superfluid, we find that our result can be well approximated by κ ∝ 1/∆ 6 at low T, where ∆ is the neutron gap, the constant of proportionality depending on the density. We further comment on the possible relevance of electron and superfluid phonon collisions in obtaining the total contribution to the thermal conductivity in the core of superfluid neutron stars.PACS numbers: 47.37.+q,95.30.Lz