The actor hinted at an "important" reveal on his official Twitter account, before breaking the news.
I will not be involved in the 50th Anniversary Episode of Dr WHO. JB— John Barrowman News (@Team_Barrowman) March 24, 2013
Barrowman previously implied that he was in talks to reprise his Who role of Captain Jack Harkness for November's celebratory episode, claiming that he was "discussing things" with the BBC.
However, the Torchwood star later played down rumours of a return, claiming that his original quotes had been "taken totally out of context" and "twisted".
Digital Spy readers recently voted on what they wanted to see in the 50th special, with the return of Barrowman's Captain Jack proving one of the most popular responses.
Doctor Who returns to BBC One with a new run of episodes this Saturday (March 30) at 6.15pm.
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Watch the stars of Doctor Who talk the 50th anniversary with Digital Spy below: