Time-averaged net photosynthetic rate (P n) under pulsed light (PL) is known to be affected by the PL frequency and duty ratio, even though the time-averaged photosynthetic photon flux density (PPFD) is unchanged. This phenomenon can be explained by considering that photosynthetic intermediates (PIs) are pooled during light periods and then consumed by partial photosynthetic reactions during dark periods. In this study, we developed a kinetic model to estimate P n of cos lettuce (Lactuca sativa L. var. longifolia) leaves under PL based on the dynamics of the amount of pooled PIs. The model inputs are average PPFD, duty ratio, and frequency; the output is P n. The rates of both PI accumulation and consumption at a given moment are assumed to be dependent on the amount of pooled PIs at that point. Required model parameters and three explanatory variables (average PPFD, frequency, and duty ratio) were determined for the simulation using P n values under PL based on several combinations of the three variables. The model simulation for various PL levels with a wide range of time-averaged PPFDs, frequencies, and duty ratios further demonstrated that P n under PL with high frequencies and duty ratios was comparable to, but did not exceed, P n under continuous light, and also showed that P n under PL decreased as either frequency or duty ratio was decreased. The developed model can be used to estimate P n under various light environments where PPFD changes cyclically.