The 66-year-old Australian actress, who plays Edna Birch's (Shirley Stelfox) sister Lily Butterfield in the rural ITV serial, is due to finish filming within the fortnight, but will remain on screen until July.
Speaking to Inside Soap about her decision to leave, she said: "I've thoroughly enjoyed playing Lily for the last couple of years, but have agreed with the producers that the time is right for me to move on."
She added: "I have a couple of new projects in the pipeline which I'm looking forward to enormously."
Charleston previously appeared in Neighbours as the iconic Madge Bishop until 2001, when her character was killed off. She went on to star in ITV's Crossroads reinvention in 2003, before joining Emmerdale for three episodes in 2006.
She was asked to return on a more permanent basis in March the following year.
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