To understand the molecular mechanism of protein folding, it is necessary to reveal the dynamics of single proteins from the unfolded state to the folding transition state. We therefore developed a new system that can detect fluorescence signals from free single proteins for extended time periods. The system enabled us to characterize a slow conformational dynamics for the unfolded state of cytochrome c. Furthermore, we proposed a method to estimate the equilibration time for the intermediate state of protein folding.