An automated system and method for programming field programmable gate arrays (FPGAS) is disclosed for implementing user-defined algorithms specified in a high level language. The system is particularly suited for use with image processing algorithms and can speed up the process of implementing and testing a fully written high-level user-defined algorithm to a matter of a few minutes, rather than the days, weeks or even months presently required using conventional software tools. The automated system includes an analyzer module and a mapper module. The analyzer determines what logic components are required and their interrelationships, and observes the relative timing between the required components and their partial products. The mapper module utilizes the output from the analyzer module and determines where the required logic components must be placed on a given target FPGA in order to reliably route, without interference, the required interconnections between various components and I/O.