Frustrated magnetic phases have been a perennial interest to theoreticians wishing to understand the energetics and behavior of quasi-chaotic systems at the quantum level. This behavior also has potentially wide applications to developing quantum data-storage devices. Several minerals are examples of such phases. Since the definition of herbertsmithite, Cu3ZnCl2(OH)6, as a new mineral in 2004 and the rapid realization of the significance of its structure as a frustrated antiferromagnetic phase with a triangular magnetic lattice, there has been intense study of its magnetic properties and those of synthetic compositional variants. In the past five years it has been recognized that the layered copper hydroxyhalides barlowite, Cu4BrF(OH)6, and claringbullite, Cu4FCl(OH)6, are also the parent structures of a family of kagome phases, as they also have triangular magnetic lattices. This paper concerns the structural behavior of claringbullite that is a precursor to the novel frustrated antiferromagnetic states that occur below 30 K in these minerals. The reversible hexagonal (P63/mmc) ↔ orthorhombic (Pnma or Cmcm) structural phase transition in barlowite at 200−270 K has been known for several years, but the details of the structural changes that occur through the transition have been largely unexplored, with the focus instead being on quantifying the low-temperature magnetic behavior of the orthorhombic phase. This paper reports the details of the structural phase transition in natural claringbullite at 100−293 K as studied by single-crystal X-ray diffraction. The transition temperature has been determined to lie between 270 and 293 K. The progressive disordering of Cu at the unusual trigonal prismatic Cu(OH)6 site on heating is quantified through the phase transition for the first time, and a methodology for refining this disorder is presented. Key changes in the behavior of Cu(OH)4Cl2 octahedra in claringbullite have been identified that suggest why the Pnma structure is likely stabilized over an alternative Cmcm structure. It is proposed that the presence of a non-centrosymmetric octahedron in the Pnma structure allows more effective structural relaxation during the phase transition than can be achieved by the Cmcm structure, which has only centrosymmetric octahedra.