When he was 15 and 16, Holgate tweeted some questionable statements. His words have been since cleared from the social media site.
The FA chose to launch an investigation into the youngsters controversial remarks on Twitter and have since concluded their study.
"Having carefully considered all of the available evidence, including his response, the tweets themselves and a response from the club, the player has been given a formal warning and directed to undertake a mandatory FA inclusion programme," said an official statement.
This is not the only FA investigation Holgate has been involved in. In a Merseyside derby in January, Holgate was alleged to have been racially abused by Liverpool's Roberto Firmino. The findings of the investigation are yet to be published.