This paper describes the first implementation of a custom micro-kernel on a ARM-FPGA platform capable of managing reconfigurable hardware parts dynamically. After describing the structure of the proposed micro-kernel, we will focus on a custom specific system task dealing with the reconfiguration management, which is associated to a dedicated scheduling mechanism. We will describe the hardware platform on which the microkernel has been ported and provide a use case application in order to demonstrate the feasibility of the approach. At the end of this paper, we will provide quantitative results in terms of reconfiguration overhead and microkernel timing performances.