The project will mark the actor's feature film directing debut.
According to The Hollywood Reporter, Harris will helm Aaron and Sarah, starring Emma Roberts and Josh Hutcherson.
The film centres on a geek and a popular girl who meet in high school and see their relationship evolve over four years.
No production start date has been announced for the film.
Harris, who stars in the CBS sitcom How I Met Your Mother, will also appear in the upcoming Smurfs movie.