During the summer of 1906 the first battalion of the 25th infantry regiment was transferred from Fort Niobrara in Nebraska to Fort Brown, a post near Brownsville, Texas at the mouth of the Rio Grande River, to protect against Mexican revolutionaries. These 167 men had outstanding credentials for service, loyalty, discipline, and bravery during battles fought in Cuba and the Philippines. Six of these Black soldiers held the Medal of Honor and 13 had been awarded citations for bravery in the Spanish-American War. More than half of the soldiers had been in uniform for more than 5 years; 25 had served in active duty for more than 10 years; and one had accrued more that 27 years.

The citizens of Brownsville were appalled and wrote William Howard Taft, the Secretary of War, requesting that he keep the White 26th infantry at Fort Brown instead. The War Department refused to repeal the order and responded to the Brownsville citizens: "The fact is that a certain amount of race prejudice between Whites and Blacks seems to have become almost universal throughout the country, and no matter where colored troops are sent there are always some who make objections to their coming."

On the night of August 13, 1906, between ten and twenty men rampaged through the streets of Brownsville, Texas, shooting indiscriminately into windows and buildings and killing a bartender and a police horse, wounding the policeman on the horse and a newspaper editor. Some evidence, including types of shells, location of raid, some alleged eyewitness accounts, linked the mayhem with some members of three companies of African-American infantry that had faced extreme prejudice and discrimination since arriving in Texas a few weeks earlier.

Despite a great deal of contradictory evidence, the townspeople of Brownsville immediately assumed that the black soldiers were responsible, and they quickly telegraphed President Roosevelt looking for redress. Roosevelt agreed with Brownsville's white citizens who argued that the government must discharge all members of these once-respected companies immediately, with no possibility of reenlistment, because the men who might possibly know something about the raid were not helping with the investigation. On November 16, 1906, Secretary of War William H. Taft, followed President Roosevelt's instructions and dishonorably discharged all 167 members of these three companies.

Roosevelt's actions outraged African-American leaders across the country. Not only did Roosevelt lose almost all of his credibility among African Americans, disagreements within the black community about how to voice this displeasure deepened already present fissures. On one side, Booker T. Washington's camp was reluctant to criticize Roosevelt publicly and remained loyal to the Republican Party; on the other side, leaders of the Niagara Movement were much more outspoken.

The Brownsville controversy caused many African Americans to question their loyalty to Roosevelt personally and to the Republican generally.