Founder of the House of Schleswig-Holstein-Sonderburg
Cadet House of Oldenburg

John was born on 25 March 1545 in Haderslev in the Duchy of Schleswig as the fourth child and third son of King Christian III of Denmark and Norway and his wife, Dorothea of Saxe-Lauenburg. When Christian III died in 1559, he left three sons. Where the eldest, Frederick II, had long ago been appointed successor to the thrones of Denmark and Norway, all three brothers were in principle equally entitled to the father's share of the duchies of Schleswig and Holstein. To avoid unfortunate divisions of the royal part of the duchies, attempts were made to find suitable positions for the younger brothers elsewhere. The middle brother, Magnus, consequently, gave up his right of inheritance when Frederick II had him placed as prince-bishop of Ösel-Wiek in Livonia.

However, the plan to secure John the post of the prince-archbishop's successor in the Archdiocese of Bremen failed due to strong competition from North German princes. Other options abroad were thwarted because Denmark needed the support of the North German princes against Sweden in the Nordic Seven Years' War, and the king could not act as a competitor in acquiring lucrative offices and benefices for his brother. Consequently, Frederick had to agree to share his father's share of the duchies with his youngest brother, and allotted him a portion of the duchies with Sonderburg (today Danish Sønderborg) as his ducal seat.

He acted actively in the Danish government, for example supporting his sister-in-law, the Queen, when his nephew, Christian IV of Denmark, was underage. There were plans for him to marry the Dowager Queen in 1588 or 1589, repudiating his second, young wife. John died in Glücksburg.