Goodwin was born in Memphis, Tennessee. Her mother, Linda (née Kantor), is a former educator and stay-at-home mom who later worked for FedEx and Apple. Her father, Tim Goodwin, formerly owned and operated a recording studio. Goodwin changed her name from "Jennifer" to "Ginnifer" to distinguish her name, and to assist in pronunciation of her name in her regional dialect. Her younger sister, Melissa Goodwin, is a stop motion animator on shows such as Robot Chicken, on which Ginnifer has also appeared as voice talent.
Ginnifer's mother is of Ashkenazi Jewish ancestry. Goodwin was raised attending synagogue on Saturdays and Unitarian church on Sundays. She was both baptized and had a Bat Mitzvah service. In her youth, Goodwin was affiliated with the North American Federation of Temple Youth, and was active in BBYO at the Jewish Community Center in Memphis. She went to school at St. Mary's Episcopal School in Memphis, Tennessee. She then graduated from Lausanne Collegiate School in 1996, then attended Hanover College (majoring in Theater) for one year before moving on to earn her Bachelor of Fine Arts from Boston University. While a student at BU, she performed in numerous student short films, as well as several college and local stage productions. Goodwin was given the "Excellence in Acting: Professional Promise Award" by the Bette Davis Foundation, and graduated with honors. After her time at Boston University, she studied in England at Stratford Upon-Avon’s Shakespeare Institute, in conjunction with the Royal Shakespeare Company. The following year she earned an "Acting Shakespeare Certificate" at London’s Royal Academy of Dramatic Art.