Working memory impairments have been reported in adults with autism spectrum disorder (ASD) and associated with functional outcomes and social difficulties. However, little is known about the developmental trajectory of working memory in youth with ASD. The current magnetoencephalography (MEG) study is the first to examine the longitudinal development over two years of working memory networks in youth with ASD. We analysed MEG data from 32 children and adolescents with and without ASD (64 datasets; 7–14 years), all tested twice at a two-year interval, during a visual n-back task, with two loads (1- and 2-back). We performed a whole-brain functional connectivity analysis to examine the networks during the successful recognition of visual stimuli. We demonstrate that youth with ASD show decreased connectivity in the theta frequency (4–7 Hz) in the higher memory load (2-back) condition compared to typically developing (TD) controls. This hypo-connected theta network was anchored in primary visual areas with connections to frontal, parietal and limbic regions. These network differences were found despite similar task performance between ASD and TD groups. Within the TD group, we found an increase in alpha (8–14 Hz) connectivity at Time 2 compared to Time 1 in both the 1- and 2-back conditions. These findings demonstrate the continued development of working memory mechanisms over middle childhood, which were not apparent in youth with ASD. Together, our findings support a network-based approach to understanding atypical neural functioning in ASD and the developmental trajectories of working memory processes over middle childhood.