This paper presents a mathematical model capable of quantitative prediction of the state of the photosynthetic apparatus of microalgae in terms of their open, closed and damaged reaction centers under variable light conditions. This model combines the processes of photoproduction and photoinhibition in the Han model with a novel mathematical representation of photoprotective mechanisms, including qE-quenching and qI-quenching. For calibration and validation purposes, the model can be used to simulate fluorescence fluxes, such as those measured in PAM fluorometry, as well as classical fluorescence indexes. A calibration is carried out for the microalga Nannochloropsis gaditana, whereby 9 out of the 13 model parameters are estimated with good statistical significance using the realized, minimal and maximal fluorescence fluxes measured from a typical PAM protocol. The model is further validated by considering a more challenging PAM protocol alternating periods of intense light and dark, showing a good ability to provide quantitative predictions of the fluorescence fluxes even though it was calibrated for a different and somewhat simpler PAM protocol. A promising application of the model is for the prediction of PI-response curves based on PAM fluorometry, together with the long-term prospect of combining it with hydrodynamic and light attenuation models for high-fidelity simulation and optimization of full-scale microalgae production systems.