The present patent document relates to a method and apparatus for an automatic clock to enable conversion for FPGA-based prototyping systems. A library or netlist is provided having a plurality of state elements of a chip design to be prototyped by a user. The chip design can have dozens of different user clocks and clock islands using these different user clocks. The state elements of an element library or netlist are converted to a circuit having one or more state elements and other logic that receive both a user clock as well as a fast global clock. With the disclosed transformations, the functionality of the original state element is maintained, and a single or low number of global clocks can be distributed in an FPGA of the prototype with user clocks generated locally on the FPGA.