Evangeline founded and ran a world development and human rights committee at her university. She has lived under a grass hut in the jungles of the Philippines with a missionary group, and has been a volunteer for children's projects since the age of 14.

Lilly was once married to Canadian hockey player Murray Hone, but is now rumoured to be engaged to her Lost co-star Dominic Monaghan. Her known nicknames include "Evi" and "Monkey". Her Lost castmates nicknamed her "Monkey" because of her ability to climb trees with ease, a skill which has been incorporated into her character. Her fellow Lost-actor Josh Holloway also calls her 'Freckles', sharing the nickname his on-screen character 'Sawyer' gave her. She is also known on set for her tomboyishness, Christian faith, and her "potty mouth".

Lilly has stated that she "live[s] in a bubble", specifying that she is not familiar with popular culture and does not watch television or own a TV set. She has also said that she would not appear in a nude scene or perform in sexual scenes that she would consider "gratuitous".

Lilly has also used her celebrity status to help promote Just Yell Fire, a video aimed at teaching teenage girls how to defend themselves against rapists. During the summer break between the first and second seasons of Lost, Lilly spent time helping the poor in Rwanda.

On December 20, 2006, Lilly's house in Kailua, Hawaii was completely destroyed by fire while she was on the "Lost" set with one of her two roommates, both of whom work as her stand-ins on the show. The second roommate was off-island at the time of the blaze, which occurred on the final day of shooting before the show’s holiday break.