Interpreting emotional expressions appropriately poses a challenge for individuals with autism spectrum disorder (ASD). In particular, difficulties with emotional processing in ASD are more pronounced in contexts where emotional expressions are subtle, automatic, and reflexive-that is, implicit. In contrast, explicit emotional processing, which requires the cognitive evaluation of an emotional experience, appears to be relatively intact in individuals with ASD. In the present study, we examined the brain activation and functional connectivity differences underlying explicit and implicit emotional processing in age- and IQ-matched adults with (n = 17) and without (n = 15) ASD. Results indicated: (1) significantly reduced levels of brain activation in participants with ASD in medial prefrontal cortex (MPFC) and superior temporal gyrus (STG) during implicit emotion processing; (2) significantly weaker functional connectivity in the ASD group in connections of the MPFC with the amygdala, temporal lobe, parietal lobe, and fusiform gyrus; (3) No group difference in performance accuracy or reaction time; and (4) Significant positive relationship between empathizing ability and STG activity in ASD but not in typically developing participants. These findings suggest that the neural mechanisms underlying implicit, but not explicit, emotion processing may be altered at multiple levels in individuals with ASD.