The film began as a murder mystery with a comic and romantic subplot, before Allen and Brickman dropped the murder plot entirely and reworked the story around the relationship between Alvy and Annie.

Allen's working title for the film was Anhedonia, a term for the inability to experience pleasure; other rejected titles included It Had to Be Jew, Rollercoaster Named Desire, Me and My Goy, and Anxiety.

The dropped murder-mystery plotline eventually resurfaced years later in Allen's 1993 film Manhattan Murder Mystery, which also starred Diane Keaton.

The role of Annie Hall was written specifically for Diane Keaton, whose real surname is Hall and who was nicknamed Annie; she and Allen had previously been in a real-life romantic relationship.

Federico Fellini was Allen's first choice for the cinema lobby cameo criticizing pop culture pundits, but after both Fellini and Luis Buñuel declined, Marshall McLuhan was cast instead, and had to travel back from Canada for reshoots.

The film features early small roles for several future stars, including Sigourney Weaver in her film debut, Jeff Goldblum, Christopher Walken, Beverly D'Angelo, and John Glover, plus a cameo appearance by author Truman Capote as himself.

Principal photography began on May 19, 1976 on Long Island's South Fork with the lobster-boiling scene, and continued intermittently for ten months, deviating frequently from the written screenplay.

The image of Alvy's childhood home located beneath a roller coaster was not in the script; Allen decided to use it on the spot after spotting the structure while scouting locations in Brooklyn with cinematographer Gordon Willis and art director Mel Bourne.

The famous scene where Alvy accidentally sneezes into a pile of cocaine was not scripted but emerged from an on-set rehearsal accident; test audiences laughed so long at it that editors had to insert a longer pause so the following dialogue wouldn't be lost.

Cinematographer Gordon Willis suggested filming the dual therapy scenes on one set divided by a wall rather than using the traditional split-screen technique.

The film's closing narration featuring the 'we all need the eggs' joke was written and recorded only two hours before a test screening.

Diane Keaton's costume look in the film—oversized blazers, vests, ties and baggy trousers—became known as the 'Annie Hall look' and influenced women's fashion in the late 1970s; although Ralph Lauren often claimed credit, only one jacket and one tie in the film actually came from his label.

Many observers, including screenwriter Marshall Brickman and executive producer Robert Greenhut, expected Star Wars to win the major Oscars that year, but Annie Hall won Best Picture, Best Director, Best Original Screenplay, and Best Actress instead.

Despite the widespread acclaim and awards, Woody Allen expressed disappointment with the finished film, saying it was originally meant to depict what happens in a man's mind, but ended up being reduced to just the relationship between his and Keaton's characters.