The ban also means European Commission staff cannot use the Chinese-owned video-sharing app on personal devices including phones that have official apps installed, the spokesperson said, confirming a report by news website Euractiv.
Employees must remove the app as soon as possible and should do so by March 15.
TikTok, whose parent company ByteDance is Chinese, has faced increasing Western scrutiny in recent months over fears about how much access Beijing has to user data.
The United States last year banned the app from federal government devices, and some US lawmakers are trying to prohibit TikTok from operating in the United States.
Last month, the Dutch government reportedly advised public officials to steer clear of the app over similar concerns.
In November, TikTok admitted some staff in China can access the data of European users.
TikTok chief executive Shou Zi Chew was in Brussels last month for talks with EU officials during which they warned TikTok to ensure the safety of European users' data.
He insisted the company was working on a "robust" system for processing Europeans' data in Europe, an EU spokesman said at the time.
TikTok said Thursday that the European Commission ban was based on mistaken ideas about its platform.
"We are disappointed with this decision, which we believe to be misguided and based on fundamental misconceptions," a spokesperson for the Chinese-owned company said, after the Commission cited data protection concerns.
TikTok has also promised to hold U.S. users' data in the United States to allay Washington's concerns.