The production of dijets in diffractive deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 61 pb-1. The dijet cross section has been measured for virtualities of the exchanged virtual photon, 5 < Q2 < 100 GeV2, and γ*p centre-of-mass energies, 100 < W < 250 GeV. The jets, identified using the inclusive kT algorithm in the γ*p frame, were required to have a transverse energy E* T,jet > 4 GeV and the jet with the highest transverse energy was required to have E* T,jet > 5 GeV. All jets were required to be in the pseudorapidity range -3.5<η* jet<0. The differential cross sections are compared to leading-order predictions and next-to-leading-order QCD calculations based on recent diffractive parton densities extracted from inclusive diffractive deep inelastic scattering data.