The European Commission President was pictured wearing traditional dress as he was honoured at the Sala dos Caplets at Coimbra University.
Mr Juncker sported the red gown and later a matching hat as he met with Portuguese President Marcelo Rebelo de Sousa.
The award was given to the chief eurocrat by the universities dean Joao Gabriel Silva, who also gave Mr Juncker a guided tour of the institution in country’s former capital city.
Video of the event appeared to show Mr Juncker looking unimpressed as it stands at the front of the audience being given his honorary degree.
The Commission President then has his traditional dress complete as he has the red hat placed on his head by the university’s dean.
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In his praise of Mr Juncker, Fernando Alves Correia, a professor of law at the institution, said the Commission chief is a “relevant personality in the construction and consolidation of the European Union”.
Professor Correia also highlighted Mr Juncker’s “own and structured political thinking”.
“His natural cordiality and affability and the unceasing pursuit of dialogue and consensus have always coexisted harmoniously with the depth of his convictions, strongly inspired by the social doctrine of the Catholic Church and embedded in the ideology of European Christian democracy,” he said.
The professor said added in his homage the University of Coimbra conveys “feelings of recognition and gratitude to a great and distinguished friend of Portugal and the Portuguese”.
Also arguing that as Luxembourg Prime Minister Mr Juncker “never haggled support for Portuguese emigrants and gave public testimony of their appreciation for the unique qualities of the Portuguese community and for the relevant contribution of the Portuguese to the development of their country”.
Despite looking uninterested by the event, Mr Juncker later tweeted: “Thank you Coimbra, thank you Portugal for making me feel at home.”