Using event-related functional magnetic resonance imaging, we identified brain regions involved in storing associations of events discontinuous in time into long-term memory. Participants were scanned while memorizing item-triplets including simultaneous and discontinuous associations. Subsequent memory tests showed that participants remembered both types of associations equally well. First, by constructing the contrast between the subsequent memory effects for discontinuous associations and simultaneous associations, we identified the left posterior parahippocampal region, dorsolateral prefrontal cortex, the basal ganglia, posterior midline structures, and the middle temporal gyrus as being specifically involved in transforming discontinuous associations into episodic memory. Second, we replicated that the prefrontal cortex and the medial temporal lobe (MTL) especially the hippocampus are involved in associative memory formation in general. Our findings provide evidence for distinct neural operation(s) that supports the binding and storing discontinuous associations in memory. We suggest that top-down signals from the prefrontal cortex and MTL may trigger reactivation of internal representation in posterior midline structures of the first event, thus allowing it to be associated with the second event. The dorsolateral prefrontal cortex together with basal ganglia may support this encoding operation by executive and binding processes within working memory, and the posterior parahippocampal region may play a role in binding and memory formation.