One of the most attractive fields in quantum-dot cellular automata (QCA) is the implementation of configurable structures. In this paper, a novel QCA structure of a configurable flip-flop (CFF) element is introduced. In a bottom-up design approach, this paper firstly proposes well-organized QCA layouts for a positive/negative clock signal generator, a level/edge pulse converter, and a bit transport/toggle storage block. In the next step, these blocks are connected in a cascade construction to form a robust and efficient flip-flop element with a comprehensive configurable capability. The simulation results demonstrate the accuracy of proposed QCA-based structures. Design capability and flexibility of the proposed CFF element are further evaluated through the synthesis of high-level circuits including registers and counters. Consequently, this new element is the best building block to be used in the next generation of configurable systems such as QCA-based FPGAs.