Electron correlations tend to generate local magnetic moments that usually order if the lattices are not too frustrated. The hexagonal compound SrRu$_2$O$_6$ has a relatively high Neel temperature but small local moments, which seem to be at odds with the nominal valence of Ru$^{5+}$ in the $t_{2g}^3$ configuration. Here, we investigate the electronic property of SrRu$_2$O$_6$ using density functional theory (DFT) combined with dynamical-mean-field theory (DMFT). We find that the strong hybridization between Ru $d$ and O $p$ states results in a Ru valence that is closer to $+4$, leading to the small ordered moment $sim1.2mu_B$. While this is consistent with a DFT prediction, correlation effects are found to play a significant role. The local moment per Ru site remains finite $sim2.3mu_B$ in the whole temperature range investigated. Due to the lower symmetry, the $t_{2g}$ manifold is split and the quasiparticle weight is renormalized significantly in the $a_{1g}$ state, while the renormalization in $e_g$ states is about a factor of 2--3 weaker. Our theoretical Neel temperature $sim700$~K is in reasonable agreement with experimental observations. SrRu$_2$O$_6$ is a unique system in which localized and itinerant electrons coexist with the proximity to an orbitally-selective Mott transition within the $t_{2g}$ sector.
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