In the mid-1960's problems with racial imbalance in some Massachusetts public school systems led to programs aimed at alleviating racial isolation. In September 1966, six towns (including Lincoln) inaugurated the METCO program by accepting students from Boston. The program continues in operation and currently enrolls approximately 3,400 students in 35 suburban school districts. METCO is the largest and second oldest continually running voluntary desegregation program in the nation.

Students from both Boston and Lincoln receive an excellent education and benefit from a level of diversity that would otherwise be absent. The program allows children of different backgrounds a chance to develop lasting friendships, talk about different issues, and solve problems together. These experiences help prepare them for a world that is increasingly multi-racial and multicultural.

Graduates from the Lincoln School usually attend the Lincoln-Sudbury Regional High School. Some go on to Boston exam schools or to private secondary schools. After high school, the students consistently go on to higher education at a rate well above that of students graduating from Boston Public Schools.