Paquin was born on 24 July 1982 in Winnipeg, Manitoba, Canada. Her father, Brian Paquin, is a Canadian retired physical education teacher, and her mother, Mary , is a New Zealand teacher of English from Wellington. Paquin is the youngest of three children, with a brother and a sister. Her father is of Dutch and French descent. Paquin has stated that all her maternal great-grandparents had immigrated to New Zealand from Ireland due to the Great Famine.
The family moved to Wellington in 1986, and Paquin attended Raphael House Rudolf Steiner School, Hutt Intermediate School and Wellington Girls' College. Her parents divorced when she was 12 years old. After moving to the United States at the age of 16, Paquin attended Windward School, where she graduated in 2000. Paquin studied for one year at Columbia College, where she lived in Carman Hall, and subsequently dropped out to continue her acting career. She holds dual New Zealand and Canadian citizenship.