The primary cilium is a crucial signaling organelle that can be generated by most human cells, and impediments to primary ciliogenesis lead to a variety of developmental disorders known as ciliopathies. The removal of the capping protein, CP110, from the mother centriole is a key early step that promotes generation of the ciliary vesicle and ciliogenesis. Recent studies have demonstrated that CP110 undergoes polyubiquitination and degradation in the proteosome, but the mechanisms of unfolding and removal from the mother centriole remain unknown. Herein we demonstrate that p97/Valosin-containing protein (VCP or Cdc48), a member of the ATPase Associated with diverse Activities (AAA) protein family, is responsible for removal of CP110 from the mother centriole. We show that use of p97 knockdown or inhibition impairs ciliogenesis, in a mechanism dependent on CP110. Our findings demonstrate a novel role for p97 in the process of primary ciliogenesis, and support a mechanism by which ubiquitinated CP110 is degraded in a process that requires p97-mediated unfolding and removal from the mother centriole.