There has been a significant amount of research investigating the design task of concept analysis, and much research on reconfigurable system design. Despite previous efforts, further research is still needed that explores how concept analysis should best be conducted for reconfigurable systems. Because reconfigurable systems have multiple configurations and different performance levels, additional information is required to understand each concept, making the design selection process more demanding. Desirable functions, concepts for each phase, and concepts for transition methods between configurations all need to be evaluated. In this paper, the fundamental challenges of reconfigurable system analysis are identified. A framework is then developed to evaluate the many options a designer may face when performing the concept analysis phase of reconfigurable system design, identifying the influence of reconfigurable systems on the process. A mini unmanned aerial vehicle case study is used to demonstrate how the framework is applied, and how existing concept analysis tools can be adapted to account for additional criteria. The paper concludes with a review of the contributions of this work and identifies areas of future work.