Recent exploration of Software-Defined Networking (SDN) for Many-Core Systems-on-Chip (MCSoCs) showed higher management flexibility and reduced physical complexity compared to other runtime communication management. In SDN, there is a software SDN Controller (control layer) that configures generic routers (data layer). The adoption of SDN makes the path establishment programmable and straightforward, according to different network policies, such as low power, QoS, fault-tolerance. It is also possible to change the path establishment policies at runtime without the need to redesign the NoC. Current works focus on proposing SDN architectures, lacking a systemic framework that describes the steps required to implement SDN into a Many-core environment. Security is an observed gap in SDN designs. A malicious task could configure SDN routers and take control of the NoC. The contribution of this work is to present a systemic and secure SDN framework (SDN-SS), detailing the steps required to support SDN in MCSoCs. This work also describes the iteration between the hardware, operating system, and user's tasks. The SDN-SS manages a Multiple-Physical NoC, with one packet-switching subnet and a set of circuitswitching subnets. The originality of SDN-SS includes (i) a step-by-step framework description addressing the phases required to support a secure SDN management; (ii) a secure SDN router configuration protocol; (iii) a protocol to change the subnet at runtime. Experimental results show the framework's capability to avoid DoS and Spoofing attacks while presents a low SDN router configuration overhead, corresponding up to 2% of a related work delay and a small impact over the user's task communication.