This paper is an interesting application of fractional order systems. Compartment models are well known and well studied in the literature. To describe the time evolution of a system undergoing reactions between populations in different compartments, often compartment models are used. These are set of differential equations coupled together. After the introduction of the fractional order derivative, fractional order models are becoming center of attraction for many researchers. But most of the fractional models are obtained just by replacing the integer order derivatives by fractional order. The main motivation is the nonlocal behavior of the fractional order derivative. In this work, the authors derive fractional order compartment models from an underlying physical stochastic process. This gives physical interpretation of the underlying fractional order model. At the end some examples are also provided by the authors to illustrate the theoretical findings.