This paper investigates the feasibility of a microalgae derived hydrogen process at a pilot scale. For that, a general transient mathematical model for managing microalgae derived hydrogen production, with temperature dependence of the cultivation medium is developed. The tool allows for the determination of the resulting whole system temperature, and mass fractions distribution. The simplified physical model combines principles of classical thermodynamics, mass, species and heat transfer, resulting in a system of differential equations which are discretized in space using a three-dimensional cell-centered finite volume scheme, namely a volume element model (VEM). A Michaelis-Menten type expression is proposed for modeling the rate of H-2 production with dependence on O-2 inhibition. Tridimensional simulations are performed in order to determine the mass fractions distributions inside a compact photobioreactor (PBR), under different operating conditions. A relatively coarse mesh was used (6048 volume elements) to obtain converged results for a large compact PBR computational domain (2 m x 5 m x 8 m). The largest computational time required for obtaining results was 560 s, i.e., less than 10 min. The numerical results for microalgal growth are validated by direct comparison to experimental measurements. Hydrogen production simulations are conducted to demonstrate PBR intermittent operation (aerobic and anaerobic stages) feasibility and adequate species evolution trends in an indirect biophotolysis approach. Therefore, after experimental validation for a particular H-2 production system, it is reasonable to state that the model could be used as an efficient tool for PBR systems thermal design, control and optimization for maximum H-2 production. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.