In September 1997, Quirke resigned his seat in the House of Assembly in order to be appointed to the Senate, filling a casual vacancy caused by the resignation of Dominic Foreman. He was elected in his own right at the 1998 federal election and was subsequently elected as a deputy whip. Quirke chaired the Select Committee on the Socio-Economic Consequences of the National Competition Policy, which was established in 1998 and reported in 2000. He supported the "Yes" vote in the 1999 Australian republic referendum.