The 51-year-old will replace Vanessa Kirby, who played the role of Princess Margaret in Season 1 and 2.
"I'm not sure which I'm more terrified about -- doing justice to the real Princess Margaret or following in the shoes of Vanessa Kirby," Bonham Carter said in a statement.
"The only thing I can guarantee is that I'll be shorter than Vanessa."
The next instalment of The Crown, expected to cover from 1964 to the late 1970s, is unlikely to hit Netflix until 2019.
For your ultimate guide on the real-life fairytales, forbidden romances and wedding day secrets of your favourite royals, including Princess Margaret, pick up a copy of the Who Collector’s Edition special, Greatest Royal Love Stories.
Want to know the truth about Picnic At Hanging Rock? We also talk about the new Wentworth, Roseanne and Santa Clarita Diet, in Episode 2 of WHO magazine's TV podcast, Binge List. Please listen on iTunes or OMNY