Systems and techniques for multiple-instantiated-module (MIM)-aware pin assignment are described. An aggregate cost function can be determined, wherein the aggregate cost function is aggregated across all instances of an MIM for placing a pin at a particular location on the boundary of the MIM. The aggregate cost function can then be used by a pin assignment engine to place the pin in the MIM. A pin assignment engine can place one pin at a time, or place multiple pins at a time by trying to optimize the aggregate cost over multiple pins. Some embodiments can propagate pin-alignment constraints through one or more instances of one or more MIMs in the circuit design layout, and then perform pin assignment while observing the pin-alignment constraints. In some embodiments, pin assignment can be performed on MIMs in decreasing order of the number of pin-alignment constraints that are imposed on the MIMs.