The network finished airing the programme's second run of episodes in July and has now announced that it will show the new instalments early next year.
Syfy's vice-president of programming and original movies Chris Regina said: "The enchanting imagination of Merlin proved very popular with our audience and we're delighted to bring the series back for a third season on Syfy."
Meanwhile, Merlin creator Johnny Capps said: "We are thrilled that Syfy will be broadcasting the third series of Merlin.
"The upcoming season will add an exciting new twist to Merlin's ongoing struggle to protect Prince Arthur, as well as thrilling audiences with bigger and bolder action sequences, stunning CGI monsters, mysterious villains and comic fun for all the family."
The series stars Colin Morgan, Bradley James, Anthony Head, Katie McGrath, Angel Coulby and Richard Wilson, while John Hurt provides the voice of the Great Dragon.
The third season will air in the UK on BBC One in September.