Fear memory persists for a long time and often causes posttraumatic stress disorder; however, the cellular mechanisms that prolong fear memory are poorly understood. Arc (also known as Arg3.1), an immediate early gene, is required for the maintenance of synaptic plasticity and long-term memory. We have previously shown that the Arc level in the mouse hippocampus increases 2 h and 12 h after contextual fear conditioning and that late Arc (at 12 h) expression contributes to memory persistence. In this study, we investigated the role of late Arc expression in spine elimination and reactivation of neuronal ensemble. We used Thy1-mGFP mice to investigate CA1 pyramidal dendritic spine density following fear conditioning. Memory persistence correlated with elimination of small mushroom spines. Inhibition of late Arc expression using Arc antisense oligodeoxynucleotide disrupted the spine elimination. We next used c-Fos-tTA ΧtetO-H2B-GFP mice to identify the neurons that had been activated during learning. CA1 neurons activated during fear conditioning were preferentially reactivated during retrieval. Inhibiting late Arc expression disrupted the population reactivated neurons. We propose that late Arc expression modifies synaptic connectivity and stabilizes neuronal ensembles related to memory engrams.