United executive vice-chairman Woodward saw flares thrown and graffiti sprayed on the gates of his Cheshire property last month by a group of supporters wearing balaclavas.
Neither Woodward or his family were at home in the village of Nether Peover at the time of the attack, which was strongly condemned by United.
The incident was widely reported but United believe The Sun had prior knowledge of the attack, with a journalist and photographer in place to cover it.
A United statement read: “Manchester United has made a formal complaint to the Independent Press Standards Organisation (Ipso) regarding The Sun newspaper and its coverage of the attack on the house of executive vice-chairman Ed Woodward.
“The complaint relates to the story ‘Ed Devils: Man Utd fans throw flares at Ed Woodward’s house in shocking scenes as anti-board protests continue to escalate’ carried online and on the back page of the print edition dated 29 January 2020.
“The club believes that The Sun had received advance notice of the intended attack, which included criminal damage and intent to intimidate, and that the journalist was present as it happened.
“The quality of the images accompanying the story indicate that a photographer was also present.
“Not only did the journalist fail to discharge the basic duty of a responsible member of society to report an impending crime and avert potential danger and criminal damage, his presence both encouraged and rewarded the perpetrators.
“We believe that this was a clear breach of both the Ipso editors’ code and journalistic ethics.
“The decision to make a formal complaint to Ipso was not taken lightly. We will await its ruling with keen interest as an important test of the self-regulatory system for newspapers and its ability to uphold ethical standards in the press.”
The Independent has contacted The Sun for comment.