Two-dimensional topological insulators are characterized by the bulk gap and one-dimensional helical states running along the edges. The theory predicts the topological protection of the helical transport from coherent backscattering. However, the unexpected deviations of the conductance from the quantized value and localization of the helical modes are generally observed in long samples. Moreover, at millikelvin temperatures significant mesoscopic fluctuations are developed as a function of the electron energy. Here we report the results of an experimental study of the transport in a HgTe quantum well with an inverted energy spectrum that reveal a multifractality of the conductance fluctuations in the helical edge state dominated transport regime. We attribute observed multifractality to mesoscopic fluctuations of the electron wave function or local density of states at the spin quantum Hall transition. We have shown that the mesoscopic two-dimensional topological insulator provides a highly tunable experimental system in which to explore the physics of the Anderson transition between topological states.