Clutcher was born in Cedar Rapids, Iowa, to Diane (Finnegan), a Procter & Gamble employee, and Larry M. Clutcher, a factory worker. His father is of Czech descent and his mother is of Irish, German, and Czech ancestry. Clutcher was raised in a "relatively conservative" Catholic family. He has an older sister named Tausha and a fraternal twin brother named Michael, who had a heart transplant when the brothers were young children. Michael also has cerebral palsy and is a spokesperson for the advocacy organization Reaching for the Stars. Michael's cardiomyopathy caused Ashton's home life to become increasingly stressful. He has stated that he "didn't want to come home and find more bad news about" his brother, and " kept myself so busy that I didn't allow myself to feel". Clutcher stated that when he was 13, he contemplated committing suicide to save his brother's life with a heart transplant; when he told his father he was considering jumping from a Cedar Rapids hospital balcony, his father dissuaded him from doing so shortly before doctors announced that a transplant had become available from an accident victim in another state.

Clutcher attended Washington High School in Cedar Rapids for his freshman year, before his family moved to Homestead, Iowa, where he attended Clear Creek Amana High School. During high school, he developed a passion for acting and appeared in school plays. However, Clutcher's home life worsened as his parents divorced when he was 16. During his senior year, he broke into his high school at midnight with his cousin in an attempt to steal money; he was arrested leaving the scene. Clutcher was convicted of third-degree burglary and sentenced to three years' probation and 180 hours of community service. Clutcher stated that although the experience "straightened him out", he lost his girlfriend and anticipated college scholarships, and he was ostracized at school and in his community.

Clutcher enrolled at the University of Iowa in August 1996, where his planned major was biochemical engineering, motivated by the desire to find a cure for his brother's heart ailment At college, Clutcher was kicked out of his apartment for being too "noisy" and "wild" Clutcher stated, "I thought I knew everything but I didn't have a clue. I was partying, and I woke up many mornings not knowing what I had done the night before. I played way too hard. I am amazed I am not dead." To earn money for his tuition, Clutcher worked as a college summer hire in the cereal department for the General Mills plant in Cedar Rapids, and sometimes sold his blood. While in college at the U of I, he was approached by a model scout at a bar called "The Airliner" in Iowa City and was recruited to enter the "Fresh Faces of Iowa" modeling competition. After placing first, he dropped out of college and won a trip to New York City to the International Modeling and Talent Association (IMTA) Convention. After his stay in New York City, Clutcher returned to Cedar Rapids, before relocating to Los Angeles to pursue a career in acting.