When stimuli are learned by repetition, they are remembered better and retained for a longer time. However, current findings are lacking as to whether the medial temporal lobe (MTL) and cortical regions are involved in the learning effect when subjects retrieve associative memory, and whether their activations differentially change over time due to learning experience. To address these issues, we designed an fMRI experiment in which face-scene pairs were learned once (L1) or six times (L6). Subjects learned the pairs at four retention intervals, 30-min, 1-day, 1-week and 1-month, after which they finished an associative recognition task in the scanner. The results showed that compared to learning once, learning six times led to stronger activation in the hippocampus, but weaker activation in the perirhinal cortex (PRC) as well as anterior ventrolateral prefrontal cortex (vLPFC). In addition, the hippocampal activation was positively correlated with that of the parahippocampal place area (PPA) and negatively correlated with that of the vLPFC when the L6 group was compared to the L1 group. The hippocampal activation decreased over time after L1 but remained stable after L6. These results clarified how the hippocampus and cortical regions interacted to support associative memory after different learning experiences.