Jun was born in Seoul, South Korea. Her mother and her mother's friends all encouraged her to be a model or actress due to her tall and slim body shape. Her childhood dream was to become a flight attendant, but later she gave up on this dream after a plane flight experience. At the age of 16, her high school friend who was a model introduced her to a photographer. Using the stage name Jun Ji-hyun, she began her career as a model for Ecole Magazine in 1997.
More than 600 guests, including celebrities, close friends and family of the star, attended her wedding to banker Choi Joon-hyuk on 13 April 2012 at Shilla Hotel in Jangchung-dong, central Seoul. Jun gave birth to the couple's first child, a boy, on 10 February 2016, around 10 a.m. She gave birth to their second son on 26 January 2018.