Houston left Howard in 1935 to serve as the first special counsel for the National Association for the Advancement of Colored People (NAACP), serving in this role until 1940. In this capacity he created litigation strategies to attack racial housing covenants and segregated schools, arguing several important civil rights cases before the U.S. Supreme Court. Through his work at the NAACP, Houston played a role in nearly every civil rights case that reached the US Supreme Court between 1930 and "Brown v. Board of Education" (1954).