Insomnia (ID) is the most common sleep disorder; however pathogenetic mechanisms underlying ID symptoms are not fully understood. Adopting a multifactorial view and considering ID a condition that involves interregional neuronal coordination would be useful to understand the ID pathophysiology. Functional connectivity (FC) may help to shed light on functional processes and neural correlates underlying ID symptoms. Despite a growing number of studies assessing FC anomalies, insight into ID pathophysiology is still fragmentary. This systematic review aims to search empirical evidence regarding FC changes in ID during resting-state. Thirty-one studies involving 1052 ID participants met the inclusion criteria for this review. Results suggested several associations between ID symptoms and impaired intra- and inter-hemispheric interactions of principal resting-state networks. Overall, evidence supported the hypothesis that a disrupted organization of the brain functional connectome characterizes ID, resulting in a decline in sleep, cognition, emotion, and memory. However, the wide methodological heterogeneity between reviewed studies and limitations in terms of study protocols and statistical approaches raised from this systematic review, makes it difficult to provide a univocal framework of ID pathophysiology. Future researches in this field should lead towards shared and rigorous search designs to ensure solid research evidence in the ID pathophysiology.