Museveni, 72, has ruled the East African nation for three decades. Critics say he has failed to tackle corruption, human rights abuses and dysfunctional public services.
Academic Stella Nyanzi, 42, a university research fellow and lecturer, called Museveni "a pair of buttocks" and his wife, who doubles as education minister, "empty-brained" in a post on her Facebook page.
Nyanzi was banned from travelling abroad last month and the state-run university where she works has begun procedures to fire her. She was arrested late on Friday before being charged on Monday, according to a charge sheet seen by Reuters.
Maria Burnett, associate director for Africa at Human Rights Watch, said the arrest and charging of Nyanzi was an "indicator that those who express critical views of the Ugandan government, especially the first family, can face its wrath."
In power since 1986, Museveni secured his latest term in office last year in a poll that independent monitors said lacked credibility and transparency.
Critics say he has placed relatives and tribal loyalists in key government and military positions and wants his son, a major general in the army, to succeed him.
Anti-government protests are rarely permitted in Uganda and are often dispersed by police beatings, teargas and the detention of activists.
Ugandan prominent academic Stella Nyanzi smiles as she stands in the dock at Buganda Road Court for criticising the wife of President Yoweri Museveni on social media, in Kampala.
The Ugandan government charged a prominent academic with a "cyber harassment" offence on Monday after she repeatedly posted criticism of President Yoweri Museveni and his wife on Facebook, according to court documents.
