Secure Function Evaluation (SFE) has received recent attention due to the massive collection and mining of personal data, but remains impractical due to its large computational cost. Garbled Circuits (GC) is a protocol for implementing SFE which can evaluate any function that can be expressed as a Boolean circuit and obtain the result while keeping each party’s input private. Recent advances have led to a surge of garbled circuit implementations in software for a variety of different tasks. However, these implementations are inefficient, and therefore GC is not widely used, especially for large problems. This research investigates, implements, and evaluates secure computation generation using a heterogeneous computing platform featuring FPGAs. We have designed and implemented SIFO: secure computational infrastructure using FPGA overlays. Unlike traditional FPGA design, a coarse-grained overlay architecture is adopted which supports mapping SFE problems that are too large to map to a single FPGA. Host tools provided include SFE problem generator, parser, and automatic host code generation. Our design allows repurposing an FPGA to evaluate different SFE tasks without the need for reprogramming and fully explores the parallelism for any GC problem. Our system demonstrates an order of magnitude speedup compared with an existing software platform.