Systems and methods of compounding of medication include a user interface that enables efficient design of compounding workflows and protocols. A user can select a workflow type from a number of workflow types differentiated at least in part by the vehicle in which a compounded pharmaceutical is to be delivered, and the user may also specify a compounding device. Options are presented and the steps of a workflow in accordance with the workflow type and options is displayed and updated in real time as options are selected. A protocol can be constructed by inserting information into the workflow based on a specification of a particular pharmaceutical to be compounded.