Cu(pz)$_2$(ClO$_4$)$_2$ (with pz denoting pyrazine C$_4$H$_4$N$_2$) is a two-dimensional spin-1/2 square-lattice antiferromagnet with $T_{mathrm{N}}$ = 4.24 K. Due to a persisting focus on the low-temperature magnetic properties, its room-temperature structural and physical properties caught no attention up to now. Here we report a study of the structural features of Cu(pz)$_2$(ClO$_4$)$_2$ in the paramagnetic phase, up to 330 K. By employing magnetization, specific heat, $^{35}$Cl nuclear magnetic resonance, and neutron diffraction measurements, we provide evidence of a second-order phase transition at $T^{star}$ = 294 K, not reported before. The absence of a magnetic ordering across $T^{star}$ in the magnetization data, yet the presence of a sizable anomaly in the specific heat, suggest a structural order-to-disorder type transition. NMR and neutron-diffraction data corroborate our conjecture, by revealing subtle angular distortions of the pyrazine rings and of ClO$^-_4$ counteranion tetrahedra, shown to adopt a configuration of higher symmetry above the transition temperature.
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