McQuarrie was born in Princeton, New Jersey. After graduating from West Windsor-Plainsboro High School South in 1986, he worked as an assistant at Christ Church Grammar School in Perth, Western Australia, recalling in 2013, “I was offered an Interim program... I picked a place out of a hat and ended up at Christ Church Grammar School. I lived at the school and worked at the boarding school, though I did very little work". Fired after nine months, "I hitchhiked for three months, came home, knocked around for about a month and then immediately started working for this detective agency.... [It] was actually a glorified security-guard position. I think in the four years I worked there I did about six investigations."
McQuarrie worked for four years at a movie theater in New Jersey as a security guard. Because the theater was in a violent area, he was often tasked to stand at the back of the room and observe the audience as they were watching the film, ensuring no fights broke out. He described the experience as "[his] film school" and "the single most educational experience [he] ever had," stating that it helped him "develop an innate sense of how the audience is responding" to a film.
