Fundamental solutions (Green’s functions) are derived for the regularised 13-moment system (R13) of rarefied gas dynamics, for small departures from equilibrium; these solutions show the presence of Knudsen layers, associated with exponential decay terms, that do not feature in the solution of lower-order systems (e.g. the Navier–Stokes–Fourier equations). Incorporation of these new fundamental solutions into a numerical framework based on the method of fundamental solutions (MFS) allows for efficient computation of three-dimensional gas microflows at remarkably low computational cost. The R13-MFS approach accurately recovers analytic solutions for low-speed flow around a stationary sphere and heat transfer from a hot sphere (for which a new analytic solution has been derived), capturing non-equilibrium flow phenomena missing from lower-order solutions. To demonstrate the potential of the new approach, the influence of kinetic effects on the hydrodynamic interaction between approaching solid microparticles is calculated. Finally, a programme of future work based on the initial steps taken in this article is outlined.