Watanabe worked as a pattern designer for Comme des Garçons under founder Rei Kawakubo after graduating from Bunka Fashion College in Tokyo. Three years later Watanabe was given command of the Comme des Garçons Tricot line and he introduced his first eponymous womens collection under the Comme des Garçons name called 'Junya Watanabe Comme Des Garçons' in 1993 and began showing in Paris that same year. In 2000, he launched his first mens collection.
His designs do reflect the principles of his mentor Kawakubo, but he takes a personal approach to his garments. He changes dramatically each season, taking a stab at futuristic designs. He gives his clothes an irregular touch through random tucking and pleating.