Obesity imposes serious health risks and involves alterations in resting‐state functional connectivity of brain networks involved in eating behavior. Bariatric surgery is an effective treatment, but its effects on functional connectivity are still under debate. In this pre‐registered study, we aimed to determine the effects of bariatric surgery on major resting‐state brain networks (reward and default mode network) in a longitudinal controlled design. Thirty‐three bariatric surgery patients and 15 obese waiting‐list control patients underwent magnetic resonance imaging at baseline, after 6 and 12 months. We conducted a pre‐registered whole‐brain time‐by‐group interaction analysis, and a time‐by‐group interaction analysis on within‐network connectivity. In exploratory analyses, we investigated the effects of weight loss and head motion. Bariatric surgery compared to waiting did not significantly affect functional connectivity of the reward network and the default mode network (FWE‐corrected p > .05), neither whole‐brain nor within‐network. In exploratory analyses, surgery‐related BMI decrease (FWE‐corrected p = .041) and higher average head motion (FWE‐corrected p = .021) resulted in significantly stronger connectivity of the reward network with medial posterior frontal regions. This pre‐registered well‐controlled study did not support a strong effect of bariatric surgery, compared to waiting, on major resting‐state brain networks after 6 months. Exploratory analyses indicated that head motion might have confounded the effects. Data pooling and more rigorous control of within‐scanner head motion during data acquisition are needed to substantiate effects of bariatric surgery on brain organization.