Cell voltage is a fundamental quantity used to monitor and control Li-ion batteries. The open circuit voltage (OCV) is of particular interest as it is believed to be a thermodynamic quantity, free of kinetic effects and history and, therefore, “simple” to interpret. Here we show that the OCV characteristics of graphite show hysteresis between charge and discharge that do not solely originate from Li dynamics and that the OCV is in fact history dependent. Combining first-principles calculations with temperature-controlled electrochemical measurements, we identify a residual hysteresis that persists even at elevated temperatures of greater than 50 °C due to differences in the phase succession between charge and discharge. Experimental entropy profiling, as well as energies and volume changes determined from first-principles calculations, suggest that the residual hysteresis is associated with different host lattice stackings of carbon and is related to Li disorder across planes in stage II configurations.