According to a statement, Hill is to pursue “new challenges”. He will leave on 30 September.
His departure comes a month after the FA integrated its sponsorship and marketing departments with those of its Wembley Stadium business as part of a wider restructure which saw the creation of the FA Group.
Hill was to lead the combined teams with Peter Daire leading sponsorship and Simon Freedman heading the marketing department under the new structure.
The FA is also looking for a new title sponsor for the FA Cup after Eon announced last week that it was not renewing its agreement with the Association after this season.
Ian Watmore, chief executive of the FA, says he is “disappointed” that Hill is to leave but praised his work on the integration of the FA and its Wembley business.