For some patients with medically refractory epilepsy (MRE), surgery is a safe and effective treatment for controlling epilepsy. However, the functional consequences of such surgery on brain activity and connectivity in children remain unknown. In the present study, we carried out a longitudinal study using resting-state functional magnetic resonance imaging in 10 children with MRE before and again at a mean of 79 days after surgery, as well as in a group of 28 healthy controls. Compared with the controls, children with epilepsy exhibited abnormalities in intrinsic activity in the thalamus, putamen, pallidum, insula, hippocampus, cerebellum, and cingulate gyrus both before and after surgery. Longitudinal analyses showed that the amplitude of low frequency fluctuations (ALFF) increased in the parietal-frontal cortex and decreased in the deep nuclei from pre- to post-surgery. The percentage changes in ALFF values in the deep nuclei were positively correlated with the age of epilepsy onset. Functional connectivity (FC) analyses demonstrated a reorganization of FC architecture after surgery. These changes in brain activity and FC after surgery might indicate that the previously disrupted functional interactions were reorganized after surgery. All these results provide preliminary evidence that the age of epilepsy onset may have some potential to predict the outcome of brain functional reorganization after surgery in children with MRE.