The actor, who portrayed Captain Jack Harkness in 'Doctor Who' and its spinoff 'Torchwood', told TV Line: "[The producers] don't want to put Jack in it. And I know fans are really upset about it, as was I."
Barrowman continued: "People have tried to say it's my schedule - it's absolutely not. I was told by the producers of 'Arrow' that if I was asked to do the 50th anniversary of Doctor Who they'd let me go and do it.
"It was nothing to do with my schedule. It's just a matter of fact that I wasn't asked."
Meanwhile, the 'Doctor Who' 50th anniversary episode recently got a whole lot scarier...
One writer on the hit BBC sci-fi show, Robert Banks Stewart, hinted that fans will see not only the return of the Zygons (as previously reported) but also appearances from the Timelord's most menacing enemies - the Daleks and the Cybermen.
Details of the plot for the anniversary episode are being kept under wraps. But the BBC have confirmed David Tennant and Billie Piper are to return for the one-off special episode.
It will be the first time Tennant has returned to his role as the tenth Doctor, which lasted from 2005 to 2010.
Piper, who played companion Rose Tyler for two series, last appeared in Tennant's final episode 'The End of Time'.
Jemma Redgrave and 'Tinker Tailor Soldier Spy' actor John Hurt have also been confirmed to co-star in the 3D anniversary show in November.