Network on Chip (NoC) is proposed as a promising solution for processors with many cores integrated onto a single chip. The main advantages of NoC are favorable scalability and high bandwidth for on-chip cores and communications. However, OS designed for NoC have not been fully researched to date. Because the microkernel operating system is composed of modules, such architecture is suitable to execute on many-core architecture. In this paper, a methodology is proposed to design and implement a microkernel-based OS on NoC. The OS is divided into modules and distributed onto the whole network using the NoC communication fabric. MINIX 3 has been extended to implement a prototype of the OS. Simulation results for real applications demonstrate that the mapping approach affects performance hugely, with the best mapping outperforming the worst with up to 43.2% reduction in average latency.