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This paper presents an analysis and comparison of the profiled results using software-based profilers (SBP) and FPGA-based profilers (FPGA-BP) for a Nios II Processor system. SBP tools are commonly used to detect performance bottlenecks of a program by applying instrumentation code at the binary level and using sampling methods for performance data gathering. This can cause the reported profiled results to be inaccurate which can mislead the embedded designer to implement the improper software function in the hardware domain. FPGA-BP tools are profilers that contain dedicated hardware that can accurately measure the performance of the software system running on a soft-core processor. They require minimal code modification and do not use any sampling techniques to collect performance data. This can provide accurate results that embedded designers can use to create an efficient and effective hardware-software partition of an embedded system.