A few studies linked air pollution to differences in functional connectivity of resting-state brain networks in children, but how air pollution exposure affects the development of brain networks remains poorly understood. Therefore, we studied the association of air pollution exposure from birth to 3 years and one year before the first imaging assessment with the development of functional connectivity across adolescence.We utilized data from 3,626 children of the Generation R Study (The Netherlands). We estimated residential exposure to PM10, PM2.5, PM2.5 absorbance, NOX, and NO2 with land-use regression models. Between- and within-network functional connectivity was calculated for 13 cortical networks, and the amygdala, hippocampus, and caudate nucleus at two assessments (8.6–12.0 and 12.6–17.1 years), resulting in 4,628 scans (2,511 for assessment 1 and 2,117 for assessment 2) from 3,626 individuals. We investigated the association between air pollution and functional connectivity with linear mixed models adjusted for life-style and socioeconomic variables, and corrected for multiple testing.Higher exposure to PM2.5 from birth to 3 years was associated with persistently lower functional connectivity over time between the amygdala and the ventral attention, somatomotor hand, and auditory networks throughout adolescence (e.g. −0.027 functional connectivity [95 % CI −0.040; −0.013] amygdala – ventral attention network per 5 μg/m3 higher PM2.5). Higher exposure to PM10 one year before the first imaging assessment was associated with persistently lower functional connectivity between the salience and medial-parietal networks throughout adolescence. Air pollution was not associated with a faster or slower change in functional connectivity with age.Air pollution exposure early in life was associated with persistent alterations in connectivity between the amygdala and cortical networks involved in attention, somatomotor, and auditory function. Concurrent exposure was associated with persistent connectivity alterations between networks related to higher cognitive functions (i.e. the salience and medial-parietal networks).