Quran Majeed is available across the world on the App Store - and has nearly 150,000 reviews.
However, Apple removed the app at the request of Chinese officials, for hosting illegal religious texts, the company said.
The Chinese government has not responded to a request for comment.
The deletion of the app was first noticed by Apple Censorship - a website that monitors apps on Apple's App Store globally.
China has been accused of human rights violations, and even genocide, against the mostly Muslim Uyghur ethnic group in Xinjiang.
Earlier this year the BBC reported that Uyghur imams had been targeted in China's Xinjiang crackdown.
Apple declined to comment, but directed the BBC to its Human Rights Policy, which states: "We're required to comply with local laws, and at times there are complex issues about which we may disagree with governments."
However, it is not clear what rules the application has broken in China. Quran Majeed says it is "trusted by over 35 million Muslims globally".
China is one of Apple's biggest markets, and the company's supply chain is heavily reliant on Chinese manufacturing.
Apple chief executive Tim Cook has been accused of hypocrisy from politicians in the US for speaking out about American politics, but staying quiet about China.
Mr Cook criticised Donald Trump's ban of seven Muslim-majority countries in 2017.
However, he is also accused of complying with the Chinese government over censorship - and not publicly criticising it for its treatment of Muslim minorities.
The New York Times reported earlier this year that Apple takes down apps in China if deemed off limits by the Chinese government. Topics that apps cannot discuss include Tiananmen Square, the Chinese spiritual movement Falun Gong, the Dalai Lama, and independence for Tibet and Taiwan.
The BBC contacted the makers of the Quran Majeed app, but has not received a response.
Another popular religious app, Olive Tree's Bible App, was also taken down this week in China - but Apple says it was withdrawn by the company.
Olive Tree did not respond to a request for comment.
Benjamin Ismail, project director at Apple Censorship, said: "Currently Apple is being turned into the censorship bureau of Beijing.
"They need to do the right thing, and then face whatever the reaction is of the Chinese government."
On Thursday, Microsoft said it was shutting down its social network, LinkedIn, in China, saying having to comply with the Chinese state had become increasingly challenging.
The decision was made after the career-networking site faced questions for blocking the profiles of some journalists.
