Gaming disorder, which is characterized by multiple cognitive and behavioral symptoms, often has comorbid psychiatric conditions such as depression and attention-deficit hyperactivity disorder. Neurobiological effects of the comorbid disorders so far reported are not converging, exhibiting positive and negative alterations of the connectivity in brain networks. In this study, we conducted resting-state functional magnetic-resonance imaging and whole brain functional connectivity analyses for young participants consisting of 40 patients diagnosed with the gaming disorder, with and without comorbid conditions, and 29 healthy controls. Compared to healthy controls, the gaming disorder-alone patients had partially diminished connectivities in the reward system and executive control network, within which there existed central nodes that served as a hub of diminished connections. In the gaming disorder patients who had comorbidity of autism spectrum disorder, the diminished connections were enlarged, with alteration of the hub nodes, to the entire brain areas involved in the reward system including cortical, subcortical and limbic areas that are crucial for reward processing, and to the whole cortical areas composing the executive control network. These observations suggest that the neurodevelopmental condition coexisting with the gaming disorder induced substantial impairment of the neural organizations associated with executive/cognitive and emotional functions, which are plausibly causal to the behavioral addiction, by rearranging and diminishing functional connectivities in the network.