The Fox Searchlight production marks the feature debut of music video director Marc Webb, reports Variety.
Clark Gregg, Minka Kelly, Matthew Gray Gubler and Rachel Boston also star in the film, based on a script by Scott Neustadter and Michael M. Weber.
The story revolves around a man (Gordon-Levitt) who falls for a woman (Deschanel) who doesn't believe in love.
Shooting began in LA on Tuesday.
Deschanel recently signed to star opposite Chloe Sevigny in indie comedy Divorce Ranch.
Gordon-Levitt will play the Cobra Commander in the upcoming GI Joe movie.