The X-ray powder diffraction (XRPD) pattern of [Mn(NH3)6](ClO4)2 at room temperature can be indexed in the regular (cubic) system (Fm $$ \overline{3} $$ m space group) with lattice cell parameter a = 11.5729 Å and with four molecules per unit cell. The XRPD pattern at 100 K is evidently different, and it indicates lowering of the crystal structure. One phase transition at $$ T_{\text{C}1}^{\text{h}} $$ = 143.5 K (on heating) and at $$ T_{\text{C}1}^{\text{c}} $$ = 137.6 K (on cooling) was detected by DSC for [Mn(NH3)6](ClO4)2 in the range of 120–300 K. The following thermodynamic parameters for phase I ↔ phase II transition were obtained: ∆H = 3.1 ± 0.2 kJ mol−1 and ∆S = 21.6 ± 0.3 J mol−1 K−1. The large value of entropy changes (∆S) indicates considerable configurational disorder in the high temperature phase. The presence of 5.9 K hysteresis of the phase transition temperature at T C and sharpness of the heat flow anomaly attest that the detected phase transition is of the first-order type. Appearing of the two new bands (splitting of δ s(HNH)F 1u mode) in FT-MIR spectra at the vicinity of 1200 cm−1 suggests that the phase transition undergoes a change of the crystal structure.