It said that the @realdonaldtrump account was "deactivated" by an employee, later clarifying that it was their last day in the job.
The account was down for 11 minutes, and Twitter is now investigating.
Mr Trump - who is an active Twitter user with 41.7 million followers - has not commented on the issue.
On Thursday evening, visitors to Mr Trump's page for a short time could only see a message that read "Sorry, that page doesn't exist!"
After the account was restored, Mr Trump's first tweet was about the Republican Party's tax cuts plan.
@POTUS, the official account of the US president, was unaffected.
Twitter said it was investigating the problem and taking steps to avoid it happening again.
It later said in a tweet: "Through our investigation we have learned that this was done by a Twitter customer support employee who did this on the employee's last day. We are conducting a full internal review."
Mr Trump joined Twitter in March 2009.
He has been actively using the social media platform to promote his policies and also attack his political opponents both during the presidential campaign in 2016 and since taking office in January.