Kowalski has said that he realized he wanted to be a writer when he was about six years old, and that he began to pursue that dream soon after. In 1988, Kowalski attended the Mercyhurst College Summer Writer's Institute, where he studied under Dr. Ken Schiff (founder of the Institute) and the late W.S. "Jack" Kuniczak. He matriculated at Boston's Emerson College in 1988, where he majored in Creative Writing, but dropped out in 1989 to devote himself to writing full-time, believing that he was focusing too much on writing at the expense of gaining the life experiences he needed to have something to write about:
"We have far too many writers in America these days who are expert stylists but who really aren't writing about anything. They can write like hell, but they don't have much to say, because they haven't done anything except study writing. As soon as I realized I was in danger of having this happen to me, I dropped out of college.... Life makes writers--nothing else does."
As a result, he took a year off from school and worked at two now-defunct Boston bookstores, Avenue Victor Hugo and Globe Corner Bookstore.
In 1990, Kowalski matriculated at St. John's College in Santa Fe, New Mexico, a four-year program whose curriculum consists of the "Great Books" of Western Civilization, including not only literature, but also philosophy, mathematics, the sciences, music and art. He believes this program made him "more well-rounded, and as a result, a more interesting person...". While at St. John's, he was the first drummer for a swing group called The Swinging Recluses, which was fronted by the late singer Lhasa de Sela and led by the current Mayor of Annapolis, Joshua J. Cohen, who also played lead saxophone. Kowalski graduated in 1994 and entered the teaching profession, leaving it in 1998 after the sale of his first novel to HarperCollins Publishers.
Kowalski has stated that his literary influences include Ernest Hemingway and John Irving, Spanish-language authors Isabel Allende and Gabriel García Márquez, and more-populist authors like spy writer John le Carré, southwestern author Tony Hillerman and sea-story writer Patrick O'Brian.