A Transport for London (TfL) spokesperson said a fire alert had closed the station.
Meanwhile, the London Fire Brigade confirmed the evacuation was sparked by a fire alarm which had gone off.
Footage showed crowds leaving the station and shutters blocking off the line to passengers.
It has since reopened.
The incident, lasting around half an hour, caused minor disruption to people’s journeys.
One person wrote on Twitter: “Fantastic journey on #Elizabeth line. Arrived at Paddington just as station was being evacuated but this must just be teething problems. Can’t wait for Bond Street to be open as closer to the office.”
Another said the incident had added an extra 15 minutes to their morning commute.
They wrote: “Tried to cut my commute by going to Paddington instead of Marylebone and getting the Elizabeth line.
“Elizabeth line at Paddington gets evacuated and I end up on the same bus I always get, with an extra 15 minutes added to my journey. Fair enough.”
Others saw the positive side of it, saying: “At least the process of evacuation works! Good practice and thankfully it was a false alarm!”
Meanwhile, another person added: “Never change, London”.
Hundreds of people had gathered at the station for a chance to get on the first train leaving for Abbey Wood just after 6.30am.