Mr Juncker made his remarks after a visit to La Zarzuela Palace which is home to King Felipe, the current Spanish monarch.
King Juan Carlos, who lived in the shadow of infamous Spanish dictator Francisco Franco for much of his life until Franco’s death in 1975, reigned until his abdication in favour of Felipe in June 2014.
He is widely credited with holding the country together as it struggled to become a democracy.
Speaking at the Carlos de Antwerp Foundation, he said: “He is a great king, I mean here, a great king of which all of Europe can be proud.”
Juan Carlos, now aged 80, was not present at the meeting, which was also attended Spanish Prime Minister Pedro Sánchez, and six of his ministers.
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During his speech, Mr Juncker – who was visibly struggling with sciatica, and who is due to fly to Washington next week to meet US President Donald Trump – warned that the rise nationalism and populism could lead to “total blindness”.
He also praised Spain’s attitude towards immigration, saying: “On this issue the signs of active solidarity impress me.”
He also suggested that Spain “has gotten back on its feet” after the severe economic turmoil which it has suffered, including high levels of unemployment.
Unemployment had declined, the budget deficit had been corrected and public debt has decreased, he stressed.
In a possible reference to Brexit, Mr Juncker said: “Ignore the siren songs that come from countries that do not want us,” adding that Spanish democracy “owes much to Europe and that the EU owes much to the energy of the Spanish people”.
Among the positive aspects of recent years in Europe, he stressed that unemployment has declined, employment has increased, the budget deficit has been corrected and public debt has decreased.
Peter Preston, a Professor of Contemporary Spanish Studies at the London School of Economics, said: “The reign of Juan Carlos de Borbón is the story of how the man nominated by Franco as the successor intended to perpetuate his dictatorship achieved massive popular legitimacy in a democracy.
“Juan Carlos threw off the shackles of the dictator’s laws and institutions and played a central role in ensuring a relatively bloodless transition to democracy.
“From 1969 to 1977, he managed to juggle the apparently incompatible objectives of fidelity to the principles of the Francoist single-party state and commitment to establishing a democratic constitutional monarchy.
“Between 1977 and 1982, he courageously defended democracy from the threat of military conspiracy.
“Thereafter, he became a national hero and acquired a popular legitimacy to which the new King can only aspire.”
(Additional reporting by Maria Ortega)