Lynskey was born in New Plymouth, New Zealand, to Kay Lynskey, a real estate agent, and Tim Lynskey, an orthopedic surgeon. She is the eldest of five children, and has three brothers and one sister. Her surname is Irish.
During her childhood, Lynskey's family moved to England for one year before returning to New Zealand. She attended New Plymouth Girls' High School, where she was involved in the drama department and school plays. After high school, Lynskey studied at Victoria University of Wellington.