He worked as an animation director on Anne of Green Gables, Sherlock Hound, Kiki's Delivery Service, Only Yesterday and Princess Mononoke.

Kondō directed the animated film Whisper of the Heart, and was expected to become one of the top directors at Studio Ghibli, alongside Hayao Miyazaki and Isao Takahata, and to become their eventual successor.

Kondo moved to Nippon Animation in June 1978, participating in the production of such shows as Future Boy Conan and Anne of Green Gables.

On March 16, 1985, Kondō resigned from his position at Telecom Animation Film, and was hospitalized from June through August for a type of pneumonia (自然気胸 shizen kikyō).

On January 21, 1998, he died suddenly of an aortic dissection in the Tachikawa City Hospital in Tokyo at age 47.