It has been claimed that the cyclic electron flow around PSI (CEF-PSI) plays an important role in protection of PSI against the fluctuating light photoinhibition. However, the photoprotective mechanism of PSI is not fully elucidated. Here, we approached the mechanism, using the two CEF-PSI mutants of Arabidopsis thaliana, and antimycin A, an inhibitor of the PGR5-mediated CEF-PSI. Dark-adapted leaves in these plants were illuminated in the fluctuating light alternating high-light at 1200 µmol m−2 s−1 and low-light at 30 µmol m−2 s−1 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 the PGR5-mediated CEF-PSI, didn’t 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. In combination with our previous report that high Y(NA) was alleviated by the enhancement of CEF-PSI, a model for the protective mechanisms of PSI are proposed. In this model, both alleviation of Y(NA) and acceleration of Y(ND) are indispensable, and for realization of such the 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.