Reconfigurable single-chip emulation systems were proposed as an alternative to multichip emulation systems. Because they cannot be emulated on a single chip at once, large designs are sliced into partitions that are downloaded and executed sequentially on the same reconfigurable emulation chip. In this paper, we address the problem of partitioning a design on a reconfigurable single-chip emulator under resource constraints. First, we extract an acyclic flow graph of the design to be emulated. Then, we model the problem as an integer linear programming problem (IP) based on the acyclic flow graph of the design where the structure of the assignment and precedence constraints produce a tight formulation. To partition a design, our algorithm uses two distinct steps with different objectives. In the first step, we minimize the number of cycles needed to schedule every look-up table (LUT) in the circuit. Then flip-flops (FFs) are inserted into the appropriate cycles of the schedule in the second step. Experiments are conducted on small- and medium-size circuits from the MCNC Partitioning93 benchmark suite. The obtained results show that our algorithm produces optimal partitioning schedules.