There is a well-established association between APOE genotype and the risk of developing Alzheimer's disease (AD). Relative to individuals with the common ε3/ε3 genotype, carriers of the ε4 allele are at increased risk of developing AD, while carriers of the ε2 allele appear to be protected against the disease. However, we recently reported that in a sample of cognitively healthy adults, both ε4 and ε2 carriers showed nearly identical changes in the pattern of fMRI activity during memory and non-memory tasks, relative to ε3 homozygotes. These findings suggest that the effects of APOE on brain function are not tightly linked to the effects of this gene on AD risk. Here we test the hypothesis that APOE has an intrinsic effect on the brain's functional networks. Resting-state fMRI was used to compare the pattern of functional connectivity of a variety of resting-state networks between 77 cognitively healthy participants aged 32 to 55 with different APOE genotypes (23 ε2/ε3, 20 ε3/ε3, 26 ε3/ε4, and 8 ε4/ε4). Differences between genotype groups were found in two hippocampal networks, the auditory network, the left frontal-parietal network, and the lateral visual network. While there was considerable variety in the brain regions affected and the direction of change across networks, the main finding was that changes in functional connectivity were similar in ε4 and ε2 carriers, relative to ε3 homozygotes. APOE appears to have an intrinsic effect on the differentiation of functional networks in the brain. This effect is apparent in cognitively healthy adults and does not manifest in a manner reflective of the link between APOE and AD risk. Rather, the effects of APOE on brain function may relate to the role of this gene in neurodevelopment.