Mathematical disabilities (MD) have a negative life‐long impact on professional success, employment, and health outcomes. Yet little is known about the intrinsic functional brain organization that contributes to poor math skills in affected children. It is now increasingly recognized that math cognition requires coordinated interaction within a large‐scale fronto‐parietal network anchored in the intraparietal sulcus (IPS). Here we characterize intrinsic functional connectivity within this IPS‐network in children with MD, relative to a group of typically developing (TD) children who were matched on age, gender, IQ, working memory, and reading abilities. Compared to TD children, children with MD showed hyper‐connectivity of the IPS with a bilateral fronto‐parietal network. Importantly, aberrant IPS connectivity patterns accurately discriminated children with MD and TD children, highlighting the possibility for using IPS connectivity as a brain‐based biomarker of MD. To further investigate regional abnormalities contributing to network‐level deficits in children with MD, we performed whole‐brain analyses of intrinsic low‐frequency fluctuations. Notably, children with MD showed higher low‐frequency fluctuations in multiple fronto‐parietal areas that overlapped with brain regions that exhibited hyper‐connectivity with the IPS. Taken together, our findings suggest that MD in children is characterized by robust network‐level aberrations, and is not an isolated dysfunction of the IPS. We hypothesize that intrinsic hyper‐connectivity and enhanced low‐frequency fluctuations may limit flexible resource allocation, and contribute to aberrant recruitment of task‐related brain regions during numerical problem solving in children with MD. We investigated intrinsic functional connectivity and regional low‐frequency signal fluctuations in a well‐characterized group of 7–9‐year old children with mathematical disabilities (MD). Compared to carefully matched typically developing peers, we found MD‐related hyper‐connectivity of the intraparietal sulcus (IPS), as well as higher levels of spontaneous low frequency fluctuations in multiple frontal and parietal areas. Our findings advance the view that MD is best characterized as a network‐level deficit, and not an isolated dysfunction of the IPS.