We report the discovery of a low temperature spin-flop transition in 5C pyrrhotite at ~155 K that is similar to those seen in hematite at 260 K and FeS (troilite) at 440 K. The 5C crystal was produced by annealing a 4C pyrrhotite crystal at 875 K, to produce a change in the vacancy-ordering scheme that developed during cooling. The 5C structure is confirmed by single crystal x-ray diffraction and the stoichiometry and homogeneity by electron microprobe and SEM BSE mapping. RUS, heat capacity and magnetisation measurements from room temperature down to 2 K are reported. The transition is marked by a steep change in elastic properties at the transition temperature, a peak in the heat capacity and weak anomalies in measurements of magnetisation. Magnetic hysteresis loops and comparison with the magnetic properties of 4C pyrrhotite suggest that the transition involves a change in orientation of moments between two different antiferromagnetic structures, perpendicular to the crystallographic c-axis at high temperatures and parallel to the crystallographic c-axis at low temperatures. The proposed structures are consistent with a group theoretical treatment that also predicts a first order transition between the magnetic structures.