It was soon reinstated.
The company has said that an employee with the ability to suspend accounts deleted it from the site on his or her last day at company.
In a tweet on Friday, Twitter said it has "implemented safeguards to prevent this from happening again". "We won't be able to share all details about our internal investigation or updates to our security measures, but we take this seriously and our teams are on it".
While the momentary outage led to a moment of frenzy and - for some - jubilation over Trump's absence on Twitter, there are serious questions being asked about what a bigger hack could do. Some Twitter users blocked by the account have sued in court, demanding access to the account's tweets, which have been deemed official public statements.
"Earlier today @realdonaldtrump's account was inadvertently deactivated due to human error by a Twitter employee".
Any access to accounts would need to be logged, especially for a VIP account.
Twitter users expressed shock regarding the temporary suspension of President Trump's account.
Free speech advocates have said that it's better to keep Trump on the platform, and it should not be up to private companies to decide whether the president has a voice there.
"I'm concerned that Twitter seems to be vastly underestimating the number of fake accounts and bots pushing disinformation".
We reached out to Twitter and a spokesperson said, "we won't have any further comment on this issue". Users can also deactivate their own accounts.
As for Mr Trump thoughts on the deactivation, he suggested his account's temporary shuttering reflected its potency. "I guess the word must finally be getting out-and having an impact".
Trump has made extensive use of messages on Twitter to attack his opponents and promote his policies both during the 2016 presidential campaign and since taking office in January.
The cycle has become a regular feature of American politics: the President tweets something inflammatory, and a backlash ensues.
Some are hailing the employee as a hero.
Just days earlier, the company had shut down the personal account of a close Trump ally, Roger Stone, after a profanity-laced tirade insulting journalists. It recently announced it was updating its rules around sexual harassment and violence-inciting tweets, prohibiting messages that glorify violence and broadening its definition of non-consensual sexual images.
Suddenly faced with the specter of a Twitter-induced nuclear conflict, some users began asking why Mr Trump's bellicose rhetoric didn't constitute abuse.
Twitter has come under fire from critics who say the company should banish Trump for violating its terms of service.