"The possibilities are limitless," said Rodriguez. "I love this iconic character and all that she represents."
Original producer Dino De Laurentiis is in charge of the remake, which is due to be released by Universal next year.
"Barbarella is the ultimate science-fiction adventure heroine - smart, strong and sexy," De Laurentiis said in a statement.
"In our vision, the future is female, and I can't wait to introduce Barbarella to a new generation of moviegoers."
Casino Royale screenwriters Neal Purvis and Robert Wade are working on the script.
The original film was a box office flop but has since achieved cult status, constantly referred to in pop culture.
It was directed by Fonda's then-husband Roger Vadim and became infamous for the opening scene, where Fonda undresses in zero gravity. Kylie Minogue recreated the iconic sequence in the video for her 1994 single Put Yourself In My Place.
Barbarella first appeared in a French graphic magazine written and illustrated by Jean-Claude Forest in 1962, and her adventures have been published around the world.
De Laurentiis has secured the rights to the cartoon creation from Jean-Claude's son Julien.
The deal will also see the first two Barbarella books be reissued, along with the publication of material previously unreleased in English.