Lilly was born in Fort Saskatchewan, Alberta, and raised in British Columbia by her mother and her father, a produce manager. She graduated from W. J. Mouat Secondary School in Abbotsford, British Columbia, where she played soccer and was vice-president of the student council.

While in college, Lilly worked as a waitress, a mechanic, and a flight attendant for Royal Airlines to pay for her tuition. She grew up Christian and her faith influenced her decision to take part in a three-week mission trip to the Philippines when she was 18. Her interest in humanitarian causes and global development led her to major in International Relations at the University of British Columbia.

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