Microfluidic biochips, also referred to “lab-on-a-chip,” have been recently proposed to integrate all the necessary functions for biochemical analyses. This technology starts a new era of biology science, where a combination of electronic and biology is first introduced. There are several types of microfluidic biochips; among them there has been a great interest in flow-based microfluidic biochips, in which the flows of liquid is manipulated using integrated microvalves. By combining several microvalves, more complex resource units such as micropumps, switches and mixers can be built. For efficient execution, the flows of liquid routes in microfluidic biochips need to be scheduled under some resource constraints and routing constraints. The execution time of a biochemical application depends strongly on the binding and scheduling result. The most previously developed binding and scheduling algorithm is based on heuristics, and there has been no method to obtain optimal results. Considering the above, we propose an optimal method by casting the problem to a clique problem. Moreover, this paper also presents some heuristic techniques for computational time reduction. Experiments demonstrate that the proposed method is able to reduce the execution time of biochemical applications by more than 15% compared with the previous approach. Moreover, the proposed heuristic method is able to produce the results at no or little cost of optimality, in significantly shorter time than the optimal method.