Emily is the daughter of Canadian poet Paul Haines and sister of Canadian television journalist Avery Haines. Her brother is Tim Haines, owner of Bluestreak Records in Peterborough, Ontario, Canada. She was born in New Delhi, India, and raised in Canada. After settling in Peterborough at the age of three, she grew up in a house rich with experimental art and musical expression. Paul would often make cassettes of rare and eclectic music for his daughter to listen to and her early influences included Carla Bley, Robert Wyatt, and later PJ Harvey. By her teens she followed her parents' footsteps by attending the Etobicoke School of the Arts. There she met Amy Millan and Kevin Drew, with whom she would later collaborate in songs for Broken Social Scene and Stars.

Haines and Millan briefly formed their first band around 1990 while at ESA, and with songs later written and recorded while at the University of British Columbia in Vancouver in 1992–1993, at Toronto in 1995, and at Co