Hierarchical partial reconfiguration for integrated circuits includes converting, using computer hardware, a first partial reconfiguration module of a circuit design into a first partial reconfiguration container, wherein the circuit design is placed and routed, loading, using the computer hardware, a first netlist into the first partial reconfiguration container, wherein the first netlist includes a first plurality of partial reconfiguration modules that are initially empty, and including, using the computer hardware, a further netlist within each of the first plurality of partial reconfiguration modules. Using the computer hardware, the first partial reconfiguration container is implemented with the first plurality of partial reconfiguration modules being implemented within the first partial reconfiguration container.