Twitter initially posted a statement saying Mr Trump's "account was inadvertently deactivated due to human error by a Twitter employee".
But in a second statement, the company revealed the outage was due to a customer support employee on their last day in the job.
Twitter said it was conducting a full internal review.
Mr Trump didn't seem too perturbed by the incident, tweeting on Friday:
The tweet was the first of many on Friday morning in Washington, with the several tweets that followed questioning why the FBI was not investigating former political rival Hillary Clinton and the Democratic Party.
Twitter has faced calls to delete Mr Trump's account before.
But Twitter hasn't budged, saying it wouldn't delete his account or tweets threatening North Korea because it was "newsworthy" and in the public interest.
Some Twitter users applauded the employee who was responsible for the stunt, while others had plenty of fun with the outage:
More about: #Twitter #Donald-Trump