The Daily Mirror reports that the Billy Mitchell actor is one of only a few members of the BBC soap's cast to reach the milestone appearance.
"Seeing as I was originally signed up for four episodes, 996 episodes later, I still haven't been found out," Fenwick said.
"I'm absolutely delighted and can't wait to tell my mum."
Fenwick made his first appearance in the show in November 1998.
The 48-year-old's 1,000th episode, which sees Billy in a scene with Jay (Jamie Borthwick), was shot on Friday and will air later in the autumn.
EastEnders executive producer Bryan Kirkwood added: "Billy is the most lovable loser on British TV and despite a thousand episodes of bad luck, the audience are still willing him to succeed."
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