Whisper of the Heart was the highest-grossing Japanese film on the domestic market in 1999, earning ¥1.85 billion in distribution income, and grossing ¥3.15 billion in total box office revenue. It grossed $34.9 million worldwide.
The review aggregator Rotten Tomatoes reported that 94% of critics have given the film a positive review based on 17 reviews, with an average rating of 7.6/10. On Metacritic, the film has a weighted average score of 75 out of 100 based on 4 critic reviews, indicating "generally favorable reviews". Time Out London included Whisper of the Heart in their Top 50 Animated Film list. It was also included in Film4's Top 25 Animated Film list. On Anime News Network, Michael Toole gave it an overall grade of A−, calling it "beautiful and evocative; a fine tale of adolescent yearning and aspiration."
General producer and screenwriter Hayao Miyazaki defended the film's ending, saying that it was his idea. Miyazaki wanted Shizuku and Seiji to "commit to something."