Flégl became a professional tennis player in 1988. In the men's singles he could not celebrate any notable successes in the course of his career, instead he concentrated on the doubles. There he was quite successful and won five double titles on the ATP World Tour and three double titles on the ATP Challenger Tour between 1990 and 1995 . In 1990 alone he won three titles with his doubles partner Daniel Vacek , after which he played with changing partners. He reached the highest ranking in the tennis world rankings in 1990 with position 466 in singles and in 1992 with position 58 in doubles.
In the individual, he could never qualify for a Grand Slam tournament. In the doubles competition he reached the second round of the French Open three times in a row and the second round of the Australian Open once . In mixed , he reached the second round of the French Open in 1992.