The bloc has gradually expanded its contacts with Myanmar since the military-backed government began introducing reforms and released opposition leader Aung San Suu Kyi after 15 years of house arrest.
But Myanmar's human rights record remains a cause for concern, notably over a recent hike in anti-Muslim violence, for the most part directed against the Rohingya Muslim minority group in the Rakhine State.
The human rights dialogue with Myanmar will include annual meetings between top diplomats from both sides to discuss "issues of mutual interest related to human rights, democratic principles and the rule of law," the EU wrote in a statement.
The agreement also lists 21 benchmarks for Myanmar to meet. These include the adoption of international human rights treaties; abolishing the death penalty; the release of political prisoners; improvements to the rule of law; and efforts to tackle discrimination.
The document makes no specific mention of the tensions with Myanmar's Rohingya community, but calls for "measures to combat and end communal violence."
Sectarian fighting broke out in 2012 between Buddhists and Rohingya Muslims in Rakhine, leaving up to 200 dead and 140,000 displaced, most of them Muslims.
Although many have lived in the Rakhine State for generations, the Rohingya are not allowed to own property and their travel is restricted.
In April, authorities refused to allow Rohingyas to register under that ethnic group when the south-east Asian country held its first census in three decades.
Rohingyas are deemed stateless under Myanmar's 1982 Citizens Act and are officially classified as Bengali, reflecting the official position that they are illegal migrants from neighbouring Bangladesh.