Knowledge flow systems are an essential component of Agricultural Knowledge and Innovation Systems (AKIS). A traditional view of a knowledge flow system would include research as a source of knowledge, extension and education as knowledge and information channels, and agricultural entrepreneurs as recipients of knowledge. More recently, this ‘linear’ view has been widely challenged, and in view of this the European Union is proposing a new approach to encouraging innovation in agriculture in the 2014-2020 programming period. This paper assesses the nature of knowledge flows through the AKIS in Hungary, and looks at the factors that encourage and discourage these. It concludes that to more effectively encourage innovation the functioning of the AKIS in Hungary must be improved and makes six recommendations: (a) a comprehensive review of the AKIS in Hungary should be conducted; (b) the present system of incentives for knowledge flow through the AKIS should be urgently reviewed; (c) future planning should be based on a state-of-the-art understanding of AKIS as multi-actor networks rather than simply as a unidirectional linear flow; (d) new models should be developed and tested on the basis of experience from other EU Member States; (e) monitoring of the performance of the AKIS in Hungary should be improved; and (f) an annual report on the performance of the AKIS should be prepared by the Hungarian government and submitted to Parliament.