In a statement, Everton chairman Carter said: "Following a number of informal meetings involving boards of directors and senior members of management, Everton are pleased to announce a formal alliance with Lincoln City.
"Here at Everton FC we have a renowned, well-developed and successful community scheme and it is clear that this new relationship will be of enormous benefit to Lincoln City, who are committed to the introduction of and establishing of their own progressive community schemes."
The link-up will also mean that The Imps will get first look at any youngsters that The Toffees release at the end of a season.