Thermal conductivity measurements were performed on several amorphous rare earth transition metal thin films of varying microstructure. The thermal conductivity perpendicular to the plane of the film, measured by the thermal comparator method, was compared with the thermal conductivity value measured parallel to the plane of the film. The latter value was obtained by converting electrical conductivity values to thermal conductivity via the Wiedemann–Franz relationship. As expected, the columnar microstructure induced during the sputter deposition of the thin films causes an anisotropy in the thermal conductivity values, with the in-plane values consistently lower than the out-of-plane values. The effect is most pronounced for the more columnar films deposited at higher pressure, for which the in-plane thermal conductivity, 0.3 W/mK, is an order of magnitude lower than the out-of-plane thermal conductivity, 4.3 W/mK. The thermal conductivity out of the plane of the film decreased with increasing deposition pressure, due to the decreasing film density.