The FA alleged Marinakis behaved improperly around the City Ground tunnel after the final whistle in Forest's 1-0 loss on Saturday.
Marinakis has until Monday to respond to the charge.
Forest's unbeaten start to the Premier League season ended after a lengthy VAR check led to Fulham being awarded a penalty that striker Raul Jimenez converted.
The hosts were further angered when VAR ruled against them in penalty claims involving Anthony Elanga and Taiwo Awoniyi while they also had a first-half effort by Chris Wood disallowed for offside.