Mr Morales said its aim included the study of imperialism and its consequences.
He said it would counteract the Army School of the Americas in Georgia which trained US allies during the Cold War.
Some of its graduates committed serious human rights abuses in the region.
The new academy is based in the city of Santa Cruz in eastern Bolivia and will initially take 100 recruits.
Speaking at the opening ceremony, Bolivia’s Defence Minister Reymi Ferreira said: “The School of Anti-Imperialism is a school that seeks to preserve life, unlike the School of the Americas, which brainwashed military officers into believing that the enemy was our people.”
He said the training centre would seek to help soldiers identify key threats to the country’s national sovereignty.
Since his inauguration in 2005, President Morales has had a relationship with the US which has been at times very tense.
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