We have investigated the local low-energy excitations in CeRu$_4$Sn$_6$, a material discussed recently in the framework of strongly correlated Weyl semimetals, by means of Ce $M_5$ resonant inelastic x-ray scattering (RIXS). The availability of both $^2$F$_\frac{5}{2}$ and $^2$F$_\frac{7}{2}$ excitations of the Ce $4f^1$ configuration in the spectra allows for the determination of the crystal-electric field parameters that explain quantitatively the temperature dependence and anisotropy of the magnetic susceptibility. The absence of an azimuthal dependence in the spectra indicates that all crystal-electric field states are close to being rotational symmetric. We show further that the non-negligible impact of the $\check A_6^0$ parameter on the ground state of CeRu$_4$Sn$_6$ leads to a reduction of the magnetic moment due to multiplet intermixing. The RIXS results are consistent with inelastic neutron scattering (INS) data and are compared to the predictions from \textsl{ab-initio} based electronic structure calculations.