Motivated by the ongoing effort to search for high-resolution signatures of quantum spin liquids, we investigate the temperature dependence of the indirect resonant inelastic x-ray scattering (RIXS) response for the Kitaev honeycomb model. We find that, as a result of spin fractionalization, the RIXS response changes qualitatively at two well-separated temperature scales,
T
L
and
T
H
, which correspond to the characteristic energies of the two kinds of fractionalized excitations,
Z
2
gauge fluxes and Majorana fermions, respectively. While thermally excited
Z
2
gauge fluxes at temperature
T
L
lead to a general broadening and softening of the response, the thermal proliferation of Majorana fermions at temperature
T
H
∼
10
T
L
results in a significant shift of the spectral weight, both in terms of energy and momentum. Due to its exclusively indirect nature, the RIXS process we consider gives rise to a universal magnetic response and, from an experimental perspective, it directly corresponds to the
K
-edge of
Ru
3
+
in the Kitaev candidate material
α
−
RuCl
3
.