Museveni, a former guerrilla leader who has led the East African country since 1986, was declared winner of the Jan. 14 election with 59% of the vote, while Wine was given 35%.
"We have decided to withdraw from their court," Wine told a news conference in the capital Kampala. "The courts are not independent, it is clear these people (judges) are working for Mr. Museveni."
She condemned attacks on political candidates, and said the State Department is "gravely concerned by harassment of and continued threats to civil society."
Tibor Nagy, the top US diplomat for Africa, tweeted the vote was "fundamentally flawed", citing the denial of accreditation to election observers and "violence and harassment of opposition figures".
The poll followed one of the most violent campaigns in years, with harassment and arrests of the opposition, attacks on the media and the deaths of at least 54 people.