In 1206, King Valdemar II and archbishop Andreas Sunonis led a raid on Ösel island, Saaremaa.

The Estonian Foreign Delegation situated in Copenhagen was the headquarter for Estonia to seek international recognition from other countries.

[9] On 5 February 1921, diplomatic relations were established with Flemming Lerche appointed envoy to Estonia with residence in Helsinki.

[10] Economically, relations were minimal as Estonia was reorganizing much of its industries and the Land Reform of 1919 only made the two countries competitors on the international agricultural market.

The Estonian government in exile was maintained by its foreign minister in-exile and representative to Denmark August Koern.

[17] From 1945 to 1964, Denmark and the Soviet Union held difficult negotiations on compensation for the Danes who had their properties in Estonia due to nationalization policies.

Ultimately, the two countries signed an agreement in February 1964 wherein the Soviets would pay Denmark 2.6 million DKK as compensation.

[18] Official contacts between Denmark and Soviet Estonia were minimal until the Singing Revolution which culminated with Danish Foreign Minister Uffe Ellemann-Jensen signing an agreement with his Estonian counterpart Lennart Meri on renewing diplomatic relations, on 24 August 1991.

[15] In the 1990s, Denmark pursued a policy which aimed at incorporating Estonia into the European Union, NATO and Council of Europe.

[25] From 2020 to 2021, 200 Danish soldiers were deployed to Tapa Army Base as part of the NATO Enhanced Forward Presence.

[30] Estonian President Lennart Meri visited Denmark in 1994,[19] Arnold Rüütel in 2004,[31] Toomas Hendrik Ilves in 2007, 2011, 2012 and 2015 and Kersti Kaljulaid in 2017.