Quantum spin liquids (QSLs) are intriguing phases of matter possessing fractionalized excitations. Several quasi-two dimensional materials have been proposed as candidate QSLs, but direct evidence for fractionalization in these systems is still lacking. In this paper, we show that the inter-plane thermal conductivity in layered QSLs carries a unique signature of fractionalization. We examine several types of gapless QSL phases - a $Z_2$ QSL with either a Dirac spectrum or a spinon Fermi surface, and a $U(1)$ QSL with a Fermi surface. In all cases, the in-plane and $c-$axis thermal conductivities have a different power law dependence on temperature, due to the different mechanisms of transport in the two directions: in the planes, the thermal current is carried by fractionalized excitations, whereas the inter-plane current is carried by integer (non-fractional) excitations. In layered $Z_2$ and $U(1)$ QSLs with a Fermi surface, the $c-$axis thermal conductivity is parametrically smaller than the in-plane one, but parametrically larger than the phonon contribution at low temperatures.
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