Wine, whose real name is Robert Kyagulanyi, had already appeared in court, charged with treason, after claims he and other opposition members had stoned Museveni’s convoy last August.
The “annoying” charge is also in relation to the treason case, according to his lawyer Asuman Basalirwa.
Wine emerged as a popular opposition figure while pursuing a successful music career. A regular critic of Museveni, he has been thwarted from performing, and was allegedly beaten by security last year before he fled the country for medical treatment.
“This government of President Museveni is in panic mode. At first it was treason and now it is annoying President Museveni. Who on earth can't be annoyed?" the pop star told Agence France Presse newswire.
"It is a ridiculous charge and am ready to challenge it in court," he added.
A conviction could be a deterrent to running for president in 2021.
This latest charge against Wine is similar to the 18-month jail sentence Ugandan activist Stella Nyanzi received last week for ‘vulgar’ posts about the president on social media.