Ellis was elected to the House of Representatives for the Division of Adelaide, South Australia at the 2004 federal election, defeating Liberal Party incumbent Trish Worth on a 2 percent two-party swing to a margin of 1.3 points, increasing to 8.5 points in 2007. The margin was reduced to 7.7 points in 2010 and to 4.0 percent in 2013.
After the 2007 election Ellis became Minister for Youth and Minister for Sport. This made her the youngest person to become an Australian government minister, a record until then held by former Prime Minister Paul Keating. In 2009 Ellis took on the portfolio of Early Childhood Education, Childcare and Youth. After the 2010 election, Ellis became the Minister for Employment Participation and Early Childhood and Childcare and the Minister for the Status of Women. For a few months prior to the 2013 Labor government defeat, Ellis was the Minister for Early Childhood, Childcare and Youth. Ellis was then elevated to shadow cabinet with the portfolios of Education and Early Childhood.