Anísio's old dream of creating an university had a new opportunity to materialize by the creation of University of Brasilia in the new Federal Capital. He had been one of its idealizers together with Darcy Ribeiro to whom Anísio gave the task to co-ordinate the project, with the support of Brazilian Society for the Progress of Science (SBPC), that gathered the whole country's scientific community.

The process of creation of that University faced the opposition of those who, as Israel Pinheiro, feared the students and the workers who were considered by him as agitators; as well as Dom Hélder Câmara whose intention were to create a Catholic University ruled by the Jesuit Order.

After these hindrances had been removed by means of the ability of those two skilled politicians, Anísio and Darcy Ribeiro could see their dream come true at last. The law that created the University was sanctioned by President João Goulart in 1961.

Darcy was nominated its Rector and Anísio its Vice-Rector. When the first one was called to lead the Civil Cabinet of the Presidency, in 1963, Anísio took over the Rectorship.