London's Metropolitan Police charged Leslie Cooper, 36, with the murder of Abdul Hadi Arwani after receiving authorisation from the Crown Prosecution Service, the public prosecutor said in a statement.
"Mr Cooper now stands charged with a criminal offence and has the right to a fair trial," it added.
Arwani, 48, was found in his car with gunshot wounds to the chest in Wembley, northwest London, on Tuesday. The investigation is being handled by counter-terrorism police.
Cooper was due to appear before London's Camberwell Green Magistrates' Court later Tuesday.
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Arwani was a preacher at a mosque in Acton, west London, between 2005 and 2011.
Police say they are "open-minded" about the motive for his killing.
Arwani's son Murhaf called his murder a "heinous" crime and appealed for anyone with information to come forward.
"My father was a very well-loved figure in west London," he said.
"He was the most peaceful man you could ever wish to meet. He did not care what your background, race or status was. He did not care if you were rich or poor. He just wanted to help people in need.