A mechanistic physiological model of the appendicularian Oikopleura dioica has been built to represent its three feeding processes (filtration, ingestion and assimilation). The mathematical formulation of these processes is based on laboratory observations from the literature, and tests different hypotheses. This model accounts for house formation dynamics, the food storage capacity of the house and the gut throughput dynamics. The half-saturation coefficient for ingestion resulting from model simulations is approximately 28 [Formula: see text] and is independent of the weight of the organism. The maximum food intake for ingestion is also a property of the model and depends on the weight of the organism. Both are in accordance with data from the literature. The model also provides a realistic representation of carbon accumulation within the house. The modelled half-saturation coefficient for assimilation is approximately 15 [Formula: see text] and is also independent of the weight of the organism. Modelled gut throughput dynamics are based on faecal pellet formation by gut compaction. Model outputs showed that below a food concentration of 30 [Formula: see text], the faecal pellet weight should represent a lower proportion of the body weight of the organism, meaning that the faecal pellet formation is not driven by gut filling. Simulations using fluctuating environmental food availability show that food depletion is not immediately experienced by the organism but that it occurs after a lag time because of house and gut buffering abilities. This lag time duration lasts at least 30 minutes and can reach more than 2 hours, depending on when the food depletion occurs during the house lifespan.