The actor, who plays Ricky Butcher on the Walford serial, handed in his notice to bosses last week and will make his departure in the summer, The Mirror reports.
Owen is following in the footsteps of his screen wife Patsy Palmer (Bianca Butcher), who is currently out of contract with EastEnders and concentrating on motherhood following the arrival of her fourth child Bertie.
A BBC spokesperson said: "Sid will be taking a short break from filming but we fully expect to see Ricky and Bianca return to Albert Square in 2012, when Patsy also returns."
In a statement, Owen explained that he plans to focus on charity work in the coming months. He commented: "I will be taking a break from EastEnders so that I can dedicate more time to Drop 4 Drop, a charity to help alleviate the global water crisis in the developing world. Ricky will definitely be returning to Walford at some point next year."
Owen has played Ricky on and off since 1988. His current stint began in 2008 when Ricky returned to Albert Square for the funeral of his father Frank, before deciding to stick around on a permanent basis.