Biofilm-based systems have attracted more attention recently as an alternative to the standard suspended-cells process for microalgae cultivation. It has also been shown that cells can be protected from photoinhibition under intense sunlight when submitted to alternately light and dark cycles. However, the biological response to light variation is not well understood. Therefore, in this work, a mechanistic model is developed based on Han’s model to describe photosynthesis and respiration dynamics that cover different cycle times and a wide range of light fractions (Light/Dark fractions). Keeping the same average light intensity, increasing the light frequency enhances growth thanks to reduced photoinhibition. Increasing light fraction improves the growth rate as both the peak light intensity and the dark period decrease. Respiration variation in intermittent light regimes is for the first time considered in this model, giving a better explanation of biofilm growth experimental data. Understanding the model response will guide strategies for growth enhancement, and further optimize biofilm reactor design and operation and eventually benefit biomass productivity.