An exemplary compounding system and method can include two pump heads for simultaneously drawing two different fluids from at least two separate input containers such that the at least two different fluids are mixed and distributed to an output container. The system can include a manifold that maintains separation of certain of the different fluids until after passing by a first pump and a second pump and/or additional pumps. A junction can be placed in the fluid line downstream of the first and second pumps and/or additional pumps such that all or some of the fluids are mixed prior to output to the output container. The method of using the system can include incorporating software that selects various fluids at certain times and sequences to ensure optimum efficiency and safety for the system, and can continue compounding actions even when an input supply container runs out or otherwise fails to supply a particular fluid/material. The method of use also includes connection of a transfer set to a housing in a manner that further ensures optimum efficiency and safety.