The tabloid’s offices were raided last week over allegations that several reports had breached a controversial national security law.
Police detained the chief editor and five other executives, and company-linked assets were frozen.
The publication had become a leading critic of the Hong Kong and Chinese leadership.
The Apple Daily management said that “in view of staff members’ safety”, it had decided “to cease operation immediately after midnight” – making Thursday’s publication the final printed edition.
UK Foreign Secretary Dominic Raab said the paper’s closure was a “chilling blow to freedom of expression in Hong Kong”.
The digital version of the 26-year old paper will no longer be updated after midnight.
A separate announcement by publisher Next Digital thanked the readers for their “loyal support” as well as its journalists, staff and advertisers.
The tabloid has long been a beacon of media freedom in the Chinese-speaking world, and is a widely read and supported by political dissents in Hong Kong.
Chinese officials have repeatedly said media freedoms in Hong Kong are respected, but are not absolute.
Ronny Tong, a member of Hong Kong’s government, accused the paper of orchestrating a political stunt in its decision to shut down.
“People around the world probably will accuse the Hong Kong government of forcing Apple Daily to close down. But the fact of the matter is, they don’t need to,” he told the BBC.
‘A knife over your head’
The closure comes after sustained pressure on the paper from the authorities.
Apple Daily founder Jimmy Lai, who has long been a critic of the Chinese Communist Party, is already in jail on a string of charges.
Last Thursday, some 500 police officers raided the publication’s newsroom, saying its reports had breached the city’s new national security law, which makes undermining the government a criminal offence.