Objective In this study, we assessed the impact of EEG-fMRI Neurofeedback (NF) training on connectivity strength and direction in bilateral motor cortices in chronic stroke patients. Most of the studies using NF or brain computer interfaces for stroke rehabilitation have assessed treatment effects focusing on successful activation of targeted cortical regions. However, given the crucial role of brain network reorganization for stroke recovery, our broader aim was to assess connectivity changes after a NF training protocol targeting localised motor areas. Approach We considered changes in fMRI connectivity after a multisession EEG-fMRI NF training targeting ipsilesional motor areas in nine stroke patients. We applied the Dynamic Causal Modeling and Parametric Empirical Bayes frameworks for the estimation of directed connectivity changes. We considered a motor network including both ipsilesional and contralesional premotor, supplementary and primary motor areas. Main results Our results indicate that NF upregulation of targeted areas (ipsilesional supplementary and primary motor areas) not only modulated activation patterns, but also had a more widespread impact on fMRI bilateral motor networks. In particular, inter-hemispheric connectivity between premotor and primary motor regions decreased, and ipsilesional self-inhibitory connections were reduced in strength, indicating an increase in activation during the NF motor task. Significance To the best of our knowledge, this is the first work that investigates fMRI connectivity changes elicited by training of localized motor targets in stroke. Our results open new perspectives in the understanding of large-scale effects of NF training and the design of more effective NF strategies, based on the pathophysiology underlying stroke-induced deficits.