Chief executive Paul Dolan said: "Bringing back the magic to Kent's oldest football tournament was high on my agenda when I took over.
"With the return of these two top teams I hope crowds will return to watch games in the competition next season."
He added: "When Gillingham and Charlton dropped out several years ago the Cup seemed to become less important."
Gillingham boss Andy Hessenthaler and Charlton manager Chris Powell are set to attend this year's final - between Dartford and Bromley - on 2 May, where an official announcement will be made.
Source: BBC Sport
Source: BBC Sport