The Irish star triumphed in the category of 'Drama Performance: Male' at Wednesday night's (January 23) National Television Awards.
"This award is a true testament to the amazing support of the public," Morgan - who is currently shooting new BBC drama Quirke opposite Gabriel Byrne - said.
"It will always be a reminder for me of the love people have for the show, the great times I had, the hard work of everyone involved and how lucky I am to be doing what I'm doing."
Morgan went on to describe his win as a "tremendous honour".
"I want to send my huge appreciation to everyone who voted for me," he concluded.
Despite rumours that Merlin could be revived for a new movie trilogy, Morgan said following his awards win that he does not expect a film version to be produced in the near future.
> Merlin review: Our verdict on the final episode
Watch Colin Morgan discuss his NTAs win below: