Resting state fMRI (rs-fMRI) permits in-vivo characterization of brain’s functional connectivity (FC). Multi-Band accelerated EPI allows to improve the temporal resolution of rs-fMRI data and, potentially, to achieve a better characterization of the brain network correlations. However, the impact of image acceleration and orientation on FC structure has not been quantified. In this work we investigated FC changes related to image acceleration effects in a test/retest rs-fMRI protocol. We found FC differences involving relevant networks, confirmed even by graph analysis of the FC maps. Our findings explore the lower bound of single-subject FC reliability and network-dependent acceleration sensitivity.