Here, we describe a microfluidic system for hypoxia assays on human cell culture models. These systems are developed to replace or reduce animal testing in biomedical basic research. The presented system uses a gas-permeable membrane as a gas-liquid interface and a micropump for media actuation to influence the oxygen content in two cell culture chambers. To apply well-defined hypoxic conditions to the cells, a good understanding of the mass transport phenomena is necessary. Therefore, a complete network model of the microfluidic system is presented. This model is validated by means of micro-particle image velocimetry (μPIV) and optical oxygen measurement with fluorescence lifetime detection. Finally, the impact of several process parameters, e.g., the gas permeability of the pump, is discussed using the developed model.