Boynton’s first professional role was as the young Beatrix Potter in the 2006 British-American film Miss Potter. Boynton has said that the first day of filming was “the best day of [her] life”. In 2007, she was nominated for the Young Artist Award for Best Performance in a Feature Film – Supporting Young Actress, for Miss Potter.

She played Posy Fossil in 2007, one of three main characters, in the BBC film Ballet Shoes. Posy is a young, ambitious ballerina who is taken under the wing of a prestigious dance academy. She did not dance in Ballet Shoes; instead a body double was used for her character’s dancing scenes. Boynton also played the role of Margaret Dashwood in the BBC serial Sense and Sensibility. In 2011, Boynton played a guest lead on Lewis. She appeared in Mo with Julie Walters and David Haig. She portrayed the mysterious model Raphina in the 2016 film Sing Street, a ghost Polly Parsons in the 2016 film I Am the Pretty Thing That Lives in the House and Countess Helena Andrenyi in the 2017 adaptation of Murder on the Orient Express.

Since 2018, Boynton has been dating her Bohemian Rhapsody co-star Rami Malek.

In February 2020, it was announced that Boynton would play Marianne Faithfull in an upcoming biopic. Production is set to begin in October of 2020 and will cover Faithfull’s rise to fame until the age of 23.