Field Programmable Gate Arrays (FPGAs) are well known platforms for implementing embedded systems due to configurability. Recently, high temperature of FPGAs is becoming a serious issue due to their higher logic density, clock frequency, and complexity. In this work we propose, implement, and evaluate an embedded system with a thermal aware operating system on the virtex-5 FPGA. It measures the temperature of the device using the system monitor IP core configured in the operating system and manages the temperature, not to violate threshold, using the task suspension feature of the operating system. A resident task in the operating system regularly checks the temperature of the device and does thermal management if needed by suspending other active tasks for a specified time slot. If this time slot is correctly chosen, the method degrades performance only 7 percent while the temperature threshold is not violated.

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