We evaluated the integrity of the cortical network in the Fmr1 knockout mouse model of fragile X syndrome (FXS) by recording micro-electrocorticogram (ECoG) activity and measuring functional connectivity, alongside the degree of clustering (modularity) and integration capacity (path length). We found that functional connectivity is increased at both the short- and long-range levels, especially in prefrontal areas in the FXS model. This correlates with a decrement in the degree of cortical network clustering, together with an anomalously high information exchange capacity at high-frequency oscillatory bands. We conclude that the cognitive deficits manifested in FXS could be associated with the state of over-synchronization of the cortical network, which is more evident at high-frequency oscillatory bands and at frontal areas of the brain.