According to Makoto Shinkai, the film's central theme is loneliness. This was inspired by the Man'yoshu, Japan's oldest collection of poems; in that volume, love was represented by the word "koi", or "lonely sadness"; more accurately, a longing for someone in solitude. Shinkai described the film as a love story towards people who feel lonely or incomplete in their social relations, but who don't feel that they need to fix this loneliness.
Makoto Shinkai, having lived for ten years in Shinjuku, wished to capture the beauty of the scenery in modern Tokyo and showcase it in a film. He set about taking thousands of photos, upon which he created storyboards for the film.
A novel coloring method was created during production: the coloring for each character was integrated with the background, a "new innovation of sorts" that mimics the refraction of light on the skin as seen in nature. This was accomplished by coloring the outline of the character, including the lines drawn for the separation of lit and shadowed surfaces, and then incorporating the background color onto the surface.
Makoto Shinkai originally envisioned Takao as a boy who wants to help people but also felt that he should have a passion for making something since creative work can be rewarding and fulfilling. He picked out shoemaking upon he realized that shoemakers assist people with walking.