In early 2006, unnamed sources told In Touch Weekly magazine that Mandy Moore and Zach Braff were engaged. Moore's representative denied the engagement.

Braff is friends with singer Lauryn Hill, who graduated from Columbia High School in 1993, the same year as Braff. Braff mentions being great childhood friends with Hill, who went to his bar mitzvah in 1988 (as he stated in the commentary of deleted scenes from the Garden State DVD, his bar mitzvah was Broadway musical-themed). Braff is also a close friend of Scrubs co-star Donald Faison, having called Faison "one of my best friends in the world" on the special features of the Scrubs DVD. Braff is also a patron for the American Red Cross as part of its "Celebrity Cabinet."