We introduce a time-dependent R-matrix theory generalised to describe double ionization processes. The method is used to investigate two-photon double ionization of He by intense XUV laser radiation. We combine a detailed B-spline-based wavefunction description in a extended inner region with a single-electron outer region containing channels representing both single ionization and double ionization. A comparison of wavefunction densities for different box sizes demonstrates that the flow between the two regions is described with excellent accuracy. The obtained two-photon double ionization cross sections are in excellent agreement with other cross sections available. Compared to calculations fully contained within a finite inner region, the present calculations can be propagated over the time it takes the slowest electron to reach the boundary.PACS numbers: 32.80. Rm, 32.80.Fb