In 2001 she met her future husband, American actor Jimmi Simpson, while co-starring in the Stephen King mini series Rose Red, and they became engaged in 2005.
On 14 April 2007 they married in a chapel overlooking a vineyard on Lake Hayes, near Queenstown, New Zealand. Also in attendance was her best friend and Rose Red co-star Emily Deschanel, who was one of her bridesmaids. Lynskey currently resides in Los Angeles with her husband.