Patterson was at a cousin's birthday party at a gymnastics club in 1994 when a coach at the gym saw her and asked her mother if she was taking lessons. When her mother said no the coach was amazed at her natural talent. Carly then began taking lessons. In 2000, Patterson participated in the Top Gym Tournament in Belgium; she won the silver medal in the all-around and the bronze medal for balance beam, which she has said is her favorite event.

At the 2001 Goodwill Games in Brisbane, Australia, she was ranked second in the all-around before the final rotation. She was suffering from a stomach illness, however, and she missed three landings on the floor exercise and finished seventh overall. Nevertheless, her balance beam routine was particularly spectacular, featuring what would become her signature double Arabian dismount (later to be named "the Patterson").

Patterson was named the U.S. Junior National All-Around champion in 2002. She had previously received fourth place