"Let me congratulate you on your decision to sign a Memorandum of Understanding aiming at finding a solution on the Ljubljanska Banka issue," Van Rompuy said in a written statement to Milanovic and Jansa.
He said today's agreement was an important step on Croatia's path towards the European Union.
"We now await the Commission's last Monitoring Report on Croatia's pre-accession preparations to be adopted end March and the finalisation of the ratification of the Accession Treaty in all national Parliaments. I am looking forward to these next steps."
Van Rompuy said this was an important moment in the relationship between Croatia and Slovenia as well as in their relations with the EU.
"Politics is about confronting changes, and European politics is about confronting them together. By choosing the path of dialogue, tenacity and compromise, you have been able to turn the page as Member States of our Union. Your constructive approach to solving bilateral issues like the maritime sea border dispute and now the Ljubljanska Banka is a sign of maturity. The way you handle them serves as an example for the whole region," Van Rompuy said in the statement after the signing of the memorandum which solves the bank issue and paves the way for the ratification of Croatia's EU accession treaty in Slovenia.
"Today's ceremony sends a clear message: issues that seemed intractable for years can be addressed. Good neighbourly relations and effective regional cooperation can be achieved. The European Union wants the countries in the region to succeed and supports them in meeting European standards in order to ultimately join the Union."