It has been claimed that the cyclic electron flow around PSI (CEF-PSI) plays an important role in protection of PSI against fluctuating light photoinhibition. However, the photoprotective mechanism of PSI is not fully elucidated. Here, we examined the mechanism, using two CEF-PSI mutants of Arabidopsis thaliana, and antimycin A, an inhibitor of the PGR5 (proton gradient regulation 5)-mediated CEF-PSI. Dark-adapted leaves in these plants were illuminated in fluctuating light alternating between high light at 1,200 µmol m s and low light at 30 µmol m s every 2 min, and PSI and PSII parameters were simultaneously measured for 160 min with 830 nm absorption and Chl fluorescence, respectively. When CEF-PSI, especially PGR5-mediated CEF-PSI, did not operate, the acceptor-side limitation of PSI, Y(NA), increased stepwise, leading to marked PSI photoinhibition. The deficiency of CFE-PSI decreased not only the electron transport rate through PSI but also the donor-side limitation of PSI, Y(ND), in high light phases. These results showed that the large Y(ND), observed only when CEF-PSI operated, contributed to suppression of PSI photoinhibition. Taken together with our previous report that high Y(NA) was alleviated by the enhancement of CEF-PSI, a model for the protective mechanisms of PSI is proposed. In this model, both alleviation of Y(NA) and acceleration of Y(ND) are indispensable, and for realization of such a situation, regulation of the electron flows, especially the PGR5-mediated CEF-PSI, plays a key role. It is important for effective protection to regulate the balance of Y(ND) and Y(NA) through CEF-PSI.