Aflatoxins (AFs) are ubiquitously found in food and animal feed. Once food is contaminated with these compounds, decontamination is often a tedious process and sometimes difficult to be achieved. Ability of probiotic microorganisms to remove AFs from various food matrices has been extensively explored. This paper proposes a mathematical model describing the mitigation process of aflatoxins by probiotics. Stability analyses of the model as well as numerical simulations were carried out to support the analytic result. The predictivity of the model indicates that the rates of formation of aflatoxin-probiotics complexes determine how fast, rigorous, and effective the mitigation of aflatoxins in a given food can be achieved. The developed model can be used to support investigations involving removal of mycotoxins in various food matrices, and to compare and contrast the effectiveness of various control strategies especially designed for decontaminating aflatoxins from food systems.