Ensaf Haidar, president of the Raif Badawi Foundation, confirmed her arrest to CNN on Wednesday.
Haidar said Badawi is charged with running the Twitter account of Waleed Abu al-Khair, a prominent human rights lawyer and her former spouse.
Al-Khair is serving a 15-year prison sentence, which Amnesty International says is "in connection with his work protecting and defending human rights in Saudi Arabia."
His Twitter account has been used recently as a platform for those campaigning for his release.
"Words are not enough for me to express how proud I am of my husband," Badawi wrote in an open letter published by the human rights group in December.
"To all those rulers and judges who have unfairly imprisoned the free, and enslaved the people, beware of the judgement you will receive from the heavens above. Woe to you who have terrorized the aggrieved out of pride."
Amnesty International called Badawi's arrest "the latest example of Saudi Arabia's utter contempt for its human rights obligations and provides further damning proof of the authorities' intent to suppress all signs of peaceful dissent."
Badawi is set to appear before a prosecutor on Wednesday, according to Amnesty.
CNN has reached out to the Saudi government, which has not yet responded to a request for a statement.