After the attack on Pearl Harbor, the government converted the center into a Federal Detention Station, monitored by the Immigration and Naturalization Service, that housed people of Japanese, German and Italian descent who were classified as "enemy aliens," including women deported from Latin America into U.S. custody[2][3] Many of the Latin American internees had been classified officially as "voluntary internees" because they had chosen to leave their home countries after their husbands had been deported to the U.S., however, their choice was in many cases motivated by the difficulties of supporting themselves and their families alone.

[4] Beginning in June 1943, the State Department arranged for the deportation of many of the internees to Japan and Germany, which helped decrease the population as authorities prepared to transfer the remaining detainees to Crystal City, Texas.

In 1969, the facility's mission changed to that of housing young male offenders sentenced under the Youth Corrections Act.

In World War II single detainees occupied dormitories while couples resided in "Victory Huts", prefabricated one room buildings with measurements of 18 square feet (1.7 m2) each.

[8] On November 8, 2012, 27-year-old John Hall, an inmate at FCI Seagoville, pleaded guilty to violating the Matthew Shepard and James Byrd Jr.

The victim sustained multiple lacerations to his face and fractured teeth as a result of Hall's unprovoked attack.