Introduction: Typical brain development is characterized by specific patterns of maturation of functional networks. Cortico-cortical connectivity generally increases, whereas subcortico-cortical connections often decrease. Little is known about connectivity changes amongst different subcortical regions in typical development. Methods: This study examined age- and gender-related differences in functional connectivity between and within cortical and subcortical regions using two different approaches. The participants included 411 six- to ten-year-old typically developing children sampled from the population-based Generation R study. Functional connectomes were defined in native space using regions of interest from subject-specific FreeSurfer segmentations. Connections were defined as: (a) the correlation between regional mean time-series; and (b) the focal maximum of voxel-wise correlations within FreeSurfer regions. The association of age and gender with each functional connection was determined using linear regression. The preprocessing included the exclusion of children with excessive head motion and scrubbing to reduce the influence of minor head motion during scanning. Results: Cortico-cortical associations echoed previous findings that connectivity shifts from short to long-range with age. Subcortico-cortical associations with age were primarily negative in the focal network approach but were both positive and negative in the mean time-series network approach. Between subcortical regions, age-related associations were negative in both network approaches. Few connections had significant associations with gender. Conclusions: The present study replicates previously reported age-related patterns of connectivity in a relatively narrow age-range of children. In addition, we extended these findings by demonstrating decreased connectivity within the subcortex with increasing age. Lastly, we show the utility of a more focal approach that challenges the spatial assumptions made by the traditional mean time series approach.