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.
Begnning 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 district announced that the Gregory-Lincoln would receive a new campus that would be on the site of the old campus.
Initially HISD planned to locate the a new campus for the High School for the Performing and Visual Arts (HSPVA) on the same site.
In 2002 the Texas Historical Commission (THC) told HISD that there were properties eligible to the placed on the National Register of Historic Places (NRHP) in the area which HISD wished to demolish houses for the new Gregory-Lincoln campus: Genesee Street to the north, Taft Street to the West, West Gray Street to the south, and Andrews street to the east.
HISD began demolishing houses anyway.
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."

A homeowner named Anthony Pizzitola, who was resident in the Braeswood area, unsuccessfully sued HISD to stop the demolition of his house and asked historian Janet Wagner to determine the probability of historic artifacts at Gregory-Lincoln because there were rumors that there was a grave site from the American Reconstruction era.
These rumors of prevented any development for several years.
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.

The current $13.5 million, 114,000-square-foot (10,600 m²) school building was financed by the $808.6 million 2002 Rebuild HISD bond.
On Monday, December 31, 2007, the two story current Gregory Lincoln building opened.
As of January 2008 it has about 500 students.
The demolition of the original campus was scheduled to begin in January 2008.
The district planned to grade the land and place an athletic field for middle school students and a playground for elementary school students.
The new school building includes digital ceiling-mounted projectors in the classrooms.

As a result of the May 2009 closing of J. Will Jones Elementary School, 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 Do
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. Begnning 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 district announced that the Gregory-Lincoln would receive a new campus that would be on the site of the old campus. Initially HISD planned to locate the a new campus for the High School for the Performing and Visual Arts (HSPVA) on the same site. In 2002 the Texas Historical Commission (THC) told HISD that there were properties eligible to the placed on the National Register of Historic Places (NRHP) in the area which HISD wished to demolish houses for the new Gregory-Lincoln campus: Genesee Street to the north, Taft Street to the West, West Gray Street to the south, and Andrews street to the east. HISD began demolishing houses anyway. 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."
A homeowner named Anthony Pizzitola, who was resident in the Braeswood area, unsuccessfully sued HISD to stop the demolition of his house and asked historian Janet Wagner to determine the probability of historic artifacts at Gregory-Lincoln because there were rumors that there was a grave site from the American Reconstruction era. These rumors of prevented any development for several years. 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.
The current $13.5 million, 114,000-square-foot (10,600 m²) school building was financed by the $808.6 million 2002 Rebuild HISD bond. On Monday, December 31, 2007, the two story current Gregory Lincoln building opened. As of January 2008 it has about 500 students. The demolition of the original campus was scheduled to begin in January 2008. The district planned to grade the land and place an athletic field for middle school students and a playground for elementary school students. The new school building includes digital ceiling-mounted projectors in the classrooms.
As a result of the May 2009 closing of J. Will Jones Elementary School, 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 Do
Gregory-Lincoln Education Center