Jenkins was born in Victorville, California, to William T. Jenkins, a U.S. Air Force officer and fighter pilot who earned a Silver Star in the Vietnam War, and Emily Roth, who later worked in San Francisco as an environmental scientist. Her older sister is Elaine Roth, her younger sister is Jessica Jenkins Murphy.
She spent her early childhood moving frequently due to her father's military service. Having lived briefly in Thailand and Germany, the family eventually settled in Lawrence, Kansas. When she was seven years old, her father died during a NATO mock dogfight at the age of 31. During a road trip from Kansas to San Francisco, her mother dropped Jenkins and her sister off at a movie theater, where they watched the original Superman starring Christopher Reeve. Jenkins found the film inspiring, and the experience sparked an interest in pursuing filmmaking as a career.
She completed kindergarten through her junior year of high school while living in Lawrence. Her mother then moved the family to Washington, D.C., where Patty completed her senior year of high school. She received her undergraduate degree in Painting from The Cooper Union for the Advancement of Science and Art in 1993, and a master's degree in directing from the American Film Institute's AFI Conservatory in 2000. While a student at AFI, Jenkins, an avid fan of the films of Pedro Almodóvar, made the 2001 short film Velocity Rules, that she describes as a cross between a superhero film and Almodóvar's tone about an accident-prone housewife.
Beginning in junior high school, Jenkins took interest in photography, painting and screen-printing. At age 20, while interning at a commercial production company, she heeded a suggestion that she could receive film training if she worked on set for free. After doing so for some months, Jenkins advanced to second assistant camera and focus puller, then spent eight years as a cameraperson. While shooting a Michael Jackson music video, her director of photography recommended that she attend the American Film Institute to learn directing. She later made a superhero short film that played at AFI Fest. There she met Brad Wyman, who later introduced her to producer Donald Kushner, leading to her directing her first feature film, Monster (2003).