We show the detection of Quasi-Periodic patterns (QPPs) in a mouse model of Alzheimer’s disease and illustrate that QPP detection was altered between wild-type and transgenic animals. We show that QPPs contributed to BOLD functional connectivity (FC) within groups and to FC differences between groups. Regression of QPPs diminished FC in co-active regions within the QPP, while anti-correlated regions became correlated. Regression of similar QPPs in wild-type and transgenic animals altered between-group FC differences by 30-50%. These findings shed light on how QPPs contribute to FC and are promising for the application of QPPs as a new pre-clinical tool.