At the outbreak of the Irish Rebellion of 1641, Plunkett attempted to remain neutral. However, in mid-1642 government troops looted and torched his home in Balrath, County Meath: Plunkett unsurprisingly thereafter gave support to the leaders of the Irish Insurgents. He played a prominent role in the foundation of the Confederation of Kilkenny, sitting as chairman at the first meeting of the Confederate Assembly and was also a member of the Confederate Supreme Council (one of six members representing the province of Leinster). Plunkett was also appointed Muster-Master general.