The Pakistan Telecommunication Authority (PTA) on Wednesday said the website had until late Friday to heed the warning, without elaborating on the content in question.
In the meantime, Wikipedia would be "degraded", disrupting and slowing access to the free online encyclopedia, which gets billions of views each month.
"Given the intentional failure on part of the platform to comply with the directions of PTA, the services of Wikipedia have been degraded for 48 hours with the direction to block/remove the reported contents," the notice said.
"In case of non-compliance by Wikipedia, the platform will be blocked within Pakistan."
The website has previously faced restrictions on some of its pages.
Freedom of speech advocates has long criticized what they say is creeping government censorship and control of Pakistan's internet and printed and electronic media.
"The ban is disproportionate, unconstitutional, and quite ridiculous," said Usama Khilji, a digital rights activist.
"This will impact students, academia, the healthcare sector, researchers, and downgrade investor confidence in Pakistan due to the uncertainty and arbitrariness of censorship," he added.
Wikipedia did not immediately respond to a request for comment from AFP.
Pakistan blocked YouTube from 2012 to 2016 after it carried a film about the Prophet Mohammed that led to violent protests across the Muslim world.
In recent years, the country has also blocked the wildly popular video-sharing app TikTok several times over "indecent" and "immoral" content.