Quasi-Periodic patterns (QPPs) represent large-scale recurring patterns in the brain, which appear as promising contributors to low frequency BOLD fluctuations. To assess the impact of QPPs on functional connectivity (FC), we used a general linear model approach to regress their contribution out of the functional images of a group of wild-type mice. We show that QPP regression diminished FC in co-active regions within the QPP, while anti-correlated regions became correlated. By calculating FC on QPP-scrubbed images, we highlight that these effects are not solely an artifact of regression. These results suggest that QPPs orchestrate dynamic correlations between resting state networks.