Her departure from the News Corporation-owned newspaper coincides with her nomination today (Friday) as a Conservative peer. The WSJ said she was leaving because of her appointment.
Wheatcroft, a well-connected former business editor at the Times and former Sunday Telegraph, is based in London where she oversees the operations of The Wall Street Journal Europe.
A spokeswoman for the WSJ confirmed Wheatcroft's departure and said she is likely to stay with the business until a replacement is found.
She said: "As Patience will soon be installed as a peer, she is stepping down from her role as editor-in-chief Europe."
Back in 2007, Wheatcroft announced that she was leaving journalism only to reverse her decision soon after. She took up her role at the WSJ in June 2009.
Michael Grade and Julian Fellowes are among the 54 new working peers announced by the government.