Resting state fMRI (rs-fMRI) provides an excellent platform for examining the amplitude of low frequency fluctuations (ALFF) and fractional amplitude of low frequency fluctuations (fALFF), which are key indices of brain functioning. However, ALFF and fALFF have been used only sporadically to study autism. rs-fMRI data from 69 children (40 autistic, mean age = 8.47 ± 2.20 years; age range: 5.2 to 13.2; and 29 non-autistic, mean age = 9.02 ± 1.97 years; age range 5.9 to 12.9) were obtained from the Autism Brain Imaging Data Exchange (ABIDE II). ALFF and fALFF were measured using CONN connectivity toolbox and SPM12, at whole-brain & network-levels. A two-sampled t-test and a 2 Group (autistic, non-autistic) × 7 Networks ANOVA were conducted to test group differences in ALFF and fALFF. The whole-brain analysis identified significantly reduced ALFF values for autistic participants in left parietal opercular cortex, precuneus, and right insula. At the network level, there was a significant effect of diagnostic group and brain network on ALFF values, and only significant effect of network, not group, on fALFF values. Regression analyses indicated a significant effect of age on ALFF values of certain networks in autistic participants. Such intrinsically different network-level responses in autistic participants may have implications for task-level recruitment and synchronization of brain areas, which may in turn impact optimal cognitive functioning. Moreover, differences in low frequency fluctuations of key networks, such as the DMN and SN, may underlie alterations in brain responses in autism that are frequently reported in the literature.