In this study, the physiological responses and kinetic parameters of Botryococcus braunii were analyzed during a highly irradiated fed-batch culture in a cylindrical photobioreactor. This work includes a model of photon distribution throughout the bioreactor, coupled with an analysis of photosynthetic performance to simulate the level of photosaturation, photolimitation, or photoinhibition during cell growth culture. Under this simulation, the kinetic and physiological behavior was evaluated during four cycles of fed-batch culture. Physiological responses showed cellular photoacclimation to high irradiance conditions, increasing the Electron Transport Rate (ETR) values 2.5 times from cycle 1 to cycle 4, while photoprotection mechanisms such as quantum yield YII and non-photochemical quenching NPQ remained efficient. The total pigment content was low compared to other studies, and a gradual decrease in Chl a, Chl b, and carotenoids was evident between each fed-batch cycle (a 25 % reduction from cycle 1 to cycle 4). Kinetics showed a gradual increase in productivity, growth rates, and nutrient consumption between cycles. The maximum biomass concentration as dry weight (4.86 ± 0.26gL−1) was obtained in cycle 4, which also showed the highest values of productivity (0.45gL−1d−1), specific growth rate (0.134 d−1) and consumption rate (NO3, PO4). The results correlate the engineering approach to the physiological characteristics of the species, indicating that it is possible to establish an efficient fed-batch system for microalgae production.