The first campus for the Lincoln Junior-Senior School was built in 1966. The original campus was a three-story brick building. It served as a neighborhood secondary school for a section of
Montrose. The school opened just as
schools were no longer legally segregated by race in the U.S. as the result of the
Civil Rights Movement. Thorne Dreyer and Al Reinert of
Texas Monthly wrote that HISD officials at the time called it "the most successfully integrated school in the city." However some white families assigned to Lincoln avoided the school by way of private school, moving to another school zone, or renting an apartment in another school zone. A parent-teacher organization was formed despite the disadvantaged backgrounds of some families. Beginning in 1969, a desegregation program, initially funded by parishioners of the First Presbyterian Church and operated by the
Emergency School Assistance Programs, a federal government initiative to support schools that racially integrated, began. The church funding paid for the first year. It was initially both a junior and senior high school, and also became the campus of Houston Community High School, an HISD magnet school. At a later point it was solely Lincoln Junior High School. In 1980 the district closed the Gregory School (now used as the
African American Library at the Gregory School) and consolidated its students, including elementary ones, into Lincoln. A document quoted in a U.S. Congressional report stated that area residents perceived the move as trying to destabilize the Fourth Ward and "The closing of Gregory and the shifting of its students to Lincoln was met with intense opposition from Fourth Ward residents." In 2000, The development attracted controversy since it used
eminent domain to seize property owned by existing residents, even though some residents expressed a reluctance to have their property seized. Betty L. Martin of the
Houston Chronicle said that some of the properties were "reputed to be of historical significance." In 2006 Houston ISD did not find any new grave sites and started development of Gregory-Lincoln. The new Gregory-Lincoln campus was scheduled to be completed by 2008. Gregory-Lincoln's elementary boundary had an increase in territory in
Midtown. As the result of the 2011 closing of
E.O. Smith Education Center, Gregory-Lincoln's middle school boundary had an increase in territory in
Downtown Houston. As part of rezoning for the 2014–2015 school year, all portions of
Midtown previously zoned to Blackshear Elementary School and all portions of Downtown previously zoned to Blackshear as well as many portions previously zoned to Bruce Elementary School were rezoned to Gregory-Lincoln for elementary school. From 2009 to 2019 each Gregory-Lincoln principal had a term of two years or fewer. Jacob Carpenter of the
Houston Chronicle used the school as an example of a low income urban school plagued by constant staff turnover, as in addition four tenths of the teachers from each school year are not present in the following one. ==Student body==