The catalytic center of photosynthetic water oxidation, the Mn4CaO5 cluster, is assembled in photosystem II (PSII) through a light-driven process called photoactivation, whose mechanism remains elusive. Here, we used rapid-scan time-resolved Fourier transform infrared (FTIR) spectroscopy combined with the attenuated total reflection (ATR) technique to monitor the photoactivation process. Rapid-scan ATR-FTIR spectra of apo-PSII with Mn2+ upon flash illumination showed spectral features typical of carboxylate stretching vibrations, which were attributed to two carboxylate ligands, D1-D170 and D1-E189, by quantum chemical calculations. The FTIR signal decayed with a time constant of ∼0.7 s, showing that the subsequent "dark rearrangement" step occurred with a low quantum yield and Mn3+ ions were mostly released during this decay. Simulation of the kinetic process provided a slow intrinsic rate of the dark rearrangement, which was attributed to a large protein conformational change. The photoassembly mechanism of the Mn4CaO5 cluster is proposed based on these findings.