A better and non-invasive characterization of the preclinical phases of Alzheimer's disease (AD) is important to advance its diagnosis and obtain more effective benefits from potential treatments. The TgF344-AD rat model has been well characterized and shows molecular, behavioral and brain connectivity alterations that resemble the silent period of the pathology. Our aim was to longitudinally investigate functional brain connectivity in established resting-state networks (RSNs) obtained by independent component analysis (ICA) in a cohort of TgF344-AD and control rats every 3 months, from 5 to 18 months of age, to cover different stages of the disease. Before each acquisition, working memory performance was evaluated by the delayed non match-to-sample (DNMS) task. Differences in the temporal evolution were observed between groups in the amplitude and shape of the somatosensorial and sensorimotor networks but not in the whole default mode network (DMN). Subsequent high dimensional ICA analysis showed early alterations in the anterior DMN subnetwork activity of TgF344-AD rats compared to controls. Performance of DNMS task was positively correlated with somatosensorial network at 5 months of age in the wild-type animals but not in the Tg-F344 rats. At different time points, DMN showed negative correlation with cognitive performance in the control group while in the transgenic group the correlation was positive. In addition, behavioral differences observed at 5 months of age correlated with alterations in the posterior DMN subnetwork. We have demonstrated that functional connectivity using ICA represents a useful biomarker also in animal models of AD such as the TgF344AD rats, as it allows the identification of alterations associated with the progression of the disease, detecting differences in specific networks even at very early stages.