Jonathon Fagge, chief executive of NHS Norwich Clinical Commissioning Group (CCG), denies assaulting Katy Fagge on 1 October in Long Stratton.
The CCG said it was agreed last November that Mr Fagge, 43, should step aside until the case is resolved.
It said it had appointed its chief finance officer, Jo Smithson, as acting chief executive.
Mr Fagge has been given what has been described as "compassionate leave".
The CCG spokesman said the allegation and Mr Fagge's forthcoming trial next month were "clearly a difficult personal situation for Mr Fagge and his family, which inevitably would have an impact on his ability to carry out his role".
He said Mr Fagge "has pleaded not guilty and strongly denies the allegations".
An NHS health chief from Norwich has stepped aside from his post to face a charge of assaulting his wife.