This article presents the main elements of the creation of the pro-innovation policy as a new public policy. For understanding this kind of policy we should analyse the structural and functional aspects this public policy. The main concept of structural description pro-innovation policy is a National Innovation System. NIS is being analysed as a sub-functional part of the political system as a whole. This sub-functional political system should also have social and institutional connections. Furthermore, pro-innovation activity is connected with the market, state, and social aspects. The pro-innovation policy and system must be based on social endogenous resources, needs, and possibilities. These are the basic factors for legitimisation and participation, which are crucial elements for the effective implementation of the pro-innovation policy.