The oldest record of a property of the Order of St. John in Slovenia dates back to 1217; it was a commandery in Melje (near Maribor). In the Slovenian territories, the next eight centuries saw the development of commanderies and estates of the Knights of St. John. The Knights brought more than just the distinct eight-pointed white cross to the Slovenian territories. Under the white Maltese cross, connections were woven and strengthened between the Order, the owner and manager of commanderies and local authorities.

Diplomatic relations between the Sovereign Order of Malta and the Republic of Slovenia were established in 1992. A Postal Agreement to cooperate in the postal services and philately was signed in 1993.

Over the years many high-level visits have been exchanged.

On the occasion of the 20th anniversary of the establishment of diplomatic relations, in 2012, the Minister of Foreign Affairs of Slovenia, Karl Erjavec, was received by the Grand Chancellor of the Order of Malta, Jean-Pierre Mazery, at the Magistral Palace in Rome.

Four years later, the Order of Malta’s Grand Master Fra’ Matthew Festing received the President of the Republic of Slovenia Borut Pahor on an official visit that stressed the desire to strengthen cooperation in the health and social care sector

On 28th November 2018, the Slovenian Deputy Prime Minister and Minister of Foreign Affairs, Miro Cerar, was received by the then Sovereign Order of Malta’s Grand Chancellor Albrecht Boeselager in the Magistral Palace. During the talks, Minister Cerar expressed his admiration for the work carried out by its association and volunteer corps in his country.

The Order of Malta’s Grand Master Fra’ Giacomo Dalla Torre del Tempio di Sanguinetto made an official visit to Slovenia in 2019 : he was received by the Slovenian President Borut Pahor, in the presidential palace. After the meeting with President Pahor, the Grand Master met the Prime Minister Marjan Šarac and by the Speaker of Parliament Dejan Židan.

In May 2022, the State Secretary at the Ministry of Foreign Affairs of the Republic of Slovenia, Stanislav Raščan, was received by the Secretary General for Foreign Affairs of the Order of Malta, Amb. Stefano Ronca. Focus of the visit the signature of a Cooperation Agreement to enable a further development of the social and humanitarian activities of the Order in the country, in the health and social field.

The President of the Republic of Slovenia, Nataša Pirc Musar, was received in December 2024 at the Magistral Palace by the Grand Master of the Sovereign Order of Malta Fra’ John Dunlap. This was the second visit to the Order of Malta by a President of the Republic of Slovenia.

The activities of the National Association and OMAS (Order of Malta Aid Slovenia) focus mainly on first-aid assistance to pilgrims at various shrines; medical assistance; distribution of food, medicines and hygiene items; school transport and accommodation for needy families and elderly people in rural and remote areas, for asylum seekers and migrants; organization of summer camps and other initiatives for Roma children. The Order’s entities in Slovenia are active in emergencies and natural disasters in the country and abroad, such as in 2020 for the Beirut explosion, in 2021 for the earthquake in Croatia, in 2023 for the severe floods in Slovenia (the worst natural disaster ever, with EUR 9.9 billion of damage) and in 2023 for the earthquake in Turkey. Since the outbreak of the conflict in Ukraine in 2022, they have also supported the Slovak rescue service, providing humanitarian aid and assisting refugees.