Abstract: State of the art techniques provide dedicated High-Level Synthesis (HLS) performance estimator tools that can give insights on performance bottlenecks, stall rate, stall cause etc., in HLS designs. These estimators often limit themselves to simple loop topologies and limited pragma use which makes them unreliable for large designs with complex datapaths. Embodiments herein provide a method and system for non-intrusive profiling for high-level synthesis HLS based applications. The method provides a cycle-accurate, fine-grained performance profiling framework that is non-intrusive and provides an end-to-end profile of the design. Such profiling tool can help the designer/DSE tool to quickly identify the performance bottlenecks and have a guided approach towards tuning it.